are you human or are you a computer program? 
really, there is nothing headcanon in considering by whom, where and when certain things are stated. Context and naunces ARE literature.
Imagine you are in 1949.
You meet the Poland US Ambassador. You ask him: what is Poland? He answers, trying to impress you: Poland in a free, indipendent nation, ancient and proud. He is right, of course. Poland was indeed a free and indipendent state.
Next week, you meet Stalin. You ask him: what is Poland? He answers, trying to impress you: Poland? Poland is mine. I control it. He is right too, of course.
So, is there a contradiction? Are one of them necessarly wrong? Is one of these people a stupid? A liar? Is Stalin a retcon?
Of course not.
Poland was an indipendent state, with its government, laws, administration, culture and traditions (and in this, different from Siberia,for example), but under strong Soviet Russia influence (and in this, different from Canada, for example).
Looking at the context we see, in the context of ME1, Saren was needed to get to the citadel to open the arms. In ME3, we see the arms opening/closing. The plot of ME1 is now questioned. Also, why are you pushing Literature? What about just straight up Narrative Coherence? Literature, while nice, is a bit to vague from what I have seen. Many people like to use abstract terms so that they can argue around definite factors and try to be correct. We are not looking at philosophical interpretation, we are looking at the logical points presented and how they interconnect (or don't interconnect depending on who shows a superior logical argument).
So, the arms couldn't open in ME1, good? Okay.
So, where is the citation/codex entry/Cutscene that allows us to see why they are opening in ME3? I am not asking for your interpretation, I just want the actual piece of information. That is it.
In addition, you seem to be pushing your own agenda by outright assuming that because the citadel is part of the catalyst (Lets Call it the Catalyst Umbrella as it more or less comprises the Citadel and Reapers) that the signals emanating from the citadel are not part of the catalyst too. How do you come to this conclusion? When 100% of the citadel is part of the catalyst, any signal emanating from the citadel is part of the catalyst as well.
This is deduction bud. In addition, you try to reason that the citadel is separate from the catalyst with no proof other than (it is still around post destroy). That logic is not really the most effective as, using it, we see that the reapers must not be reapers because their bodies are still around post destroy. And yeah, the citadel post destroy was pretty banged up at the end bud.
As for your country example.
If politician A says Poland was (key note here in the word was) a Sovereign state, and we see it is directly controlled by Russia - no real contradiction.
However, if (assuming no propaganda) Politician A says Poland is an independent state, but then hear Stalin say it is actually his - we have a contradiction we need to look into. One supersedes the other and - upon review - we find the latter statement it the true one, which is what I have been saying. Both statements are NOT mutually exclusive. The catalyst on the citadel in ME1 CANNOT exist at the time Sovereign needed Saren to open the arms when we see the keepers can open the arms via the citadel's signals (which are - again - part of the catalyst). The issue with the catalyst though, is that while it supersedes ME1, it directly breaks the plot of ME1.
EDIT: Also, from what we know of the requirements for a state to be sovereign is that it should neither dependent on nor subjected to any other power or state. If the Poland guy says Poland is Sovereign, but we find Russia is influencing them heavily, we derive that the Poland guy is lying or dumb.
Here is my example. The Villain needs to gain access to an orb of great power to take over the universe. However, the orb is guarded by sentry's that he must get past. The Hero defeats the villain in a great fight. Then, in the next installment we find that the villain was just a pawn of the real villain who wanted the orb and was in control of the sentries the entire time.
What this is called is a continuity issue. And it does break narrative coherence. You can fill this in with your interpretation to make it work, but that is not explicitly represented in the material.
Option A: exactly.
Probably, the best method I have to discover if you can swim or not is to throw you in a very deep pool. If you swim, I'll conclude you can swim. If you drown, I'll conclude you can't (99,999% certain). Almost infallible. Doubt it? Wanna try? 
Option B: yes, and reapers corpses are not reapers as "harvested races". They are just empty shells. You can probably pick them up and do something else with them. For example: the heart or the brain of the baby reapers was 100% part of him, right? Shepard killed the baby reapers, the brain/heart is taken away and in the end used to build the crucible.
A circular fallacy does not reinforce your postulation that this is logical interpretation buddy. Please look into this further. But to go with the swimming example. If one day you jump in the water (having never swam before) and you are able to swim, you are correct, we can deduce you can swim.
However, if the next day you jump into the water only to be unable to swim. We have a continuity issue. Also, the analogy you presented does not really sum up the argument that well. I get you are trying to say you INFER the swimming ability just as you are trying to infer the catalysts control/ability over the citadel. However, if the arms were not opening/closing/platforms raising in ME3 I would be all for this as the information would not contradict itself.
Now, I have a funny feeling you will try to counter with "the reapers re-enabled this when they took the citadel". Do you have a source stating this? Headcanon is any kind of reader interpretation that is not explicitly reinforced by the lore. It may sound logical to you, but with no proof, you have no argument. Remember, it isn't what you know - it is what you can prove.
You did say that the information did not require any headcanon and was in the material itself.
As for option B. This is the redefinition fallacy at its finest mixed with headcanon. Please keep to the lore. These corpse creatures are called reapers. Their bodies are reaper bodies. You are trying to drag the conversation into a subjective arena and I can easily see it coming. And yes, 100% of the heart/brain was part of the baby reaper. The was reaper "destroyed" and is inactive (because plot) and is then re-purposed. In all reality, this does create a continuity error since we know that 100% of reaper tech indoctrinates. Not having indoctrination does not mean that "it was safe" it means that the writers did not really pay attention to their material. Conversely, we know that indoctrination is a signal and somewhat visual. The signal could have been disabled (then again, I really have no proof on this and it is pure headcanon by me) As there is no real known way to disable the indoctrination signal - except the red ending.
Sorry, bit of a tangent there. Suffice to say ME2 was not the most informative on continuity and logical process, ME3 was even less so.
A being part of B
=/=
A = B
This is basic epistemology.
All your comments are based on this epistemological mistake: the keepers answer only to the citadel. The citadel is part of the catalyst. So keepers should answer to the catalyst.
You read it as it was: the keepers answer only to the citadel. The citadel is the catalyst. So the keepers sholud answer to the catalyst.
But the citadel and the catalyst are different, indipendent concept. They can overlapp, they can be stricly connected, but they are not the same ontological thing. One is a space station, and the other one is an AI.
Vigil was referring to the space station. Circuits, metal and vats. Not the self-aware data file living in there.
The citadel send the signal to the keepers, not the catalyst.
The citadel being part of the catalyst is something totally irrelevant.
Because the citadel is not the catalyst.
You are right in that A (the citadel) being part of B (the catalyst) does not mean that The Citadel IS the Catalyst. However, you either did not read my wording or are just responding to argue here. This is what I literally said
You seem to constantly mis-read what I am writing. The catalyst is not controlling the citadel, it is the keepers that do this (that is what I have been showing you through cut scenes and codex entries). And the Keepers respond to the signals emanating from the Citadel, which 100% of the citadel is part of the Catalyst.
100% of the Citadel is PART OF the Catalyst and that Citadel has signals emanating from it. Those signals too, are PART of the Catalyst. Signals like opening/closing the arms & raising the platforms that are sent to the keepers who operate and maintain the citadel. If you can present me with an in game citation showing the keepers do not respond to signals from the citadel - you win. Otherwise, I don't think it works for you. Please pay attention as I do hate to repeat myself.
As for Vigil, yes I get it, he was talking about the space station. However, that space station - as we later find - is PART OF the Main Antagonists and was a key point in the plot of the first installment. The level of overlap the citadel has to the catalyst is not really necessary (even though you keep placing emphasis on it through a false comparison fallacy) as we know that all of the citadel is a portion of the catalyst umbrella (the other being the reapers) and that citadel has signals emanating from it, that the keepers respond to.
Personally, I prefer objective logic to philosophical debates.
cleaner that way. However, if you want to invoke epistemology, you may need to leverage fewer fallacies and more deductive (or where applicable inductive) logical models. I don't want to be mean to epistemology, I just prefer logical models over philosophical ones. However, you are correct in your representation of epistemology in that it separates truth from belief relative to knowledge. For something to be epistemologically (that is probably spelt incorrectly) true it has to be actually known and cannot be false (taken as absolute and not an interpretation of it). Source
Thus, that is why I only look at the absolute information first and see how it interconnects rather than build an interpretation that makes it connect. What we know is the following:
- The keepers respond to signals emanating from the citadel only
- The citadel is part of the catalyst (the other part being the reapers which it controls absolutely)
- The keepers would be able to respond to the catalysts as the entire citadel (and those signals emanating from it) was already a part of the catalyst.
OR, we can look at the relationship the catalyst has to the Reapers (the other part of it) and see how it interacts with that part and apply to the other part. If the catalyst controls the reapers (who are part of it) this would fuel the belief that it could control the citadel. This belief is then validated when we see it operating the arms and the platforms. With no additional context we derive that yes, the catalyst controls the citadel (how? It could be via keepers or directly. The former is explicit, the latter is inferred).
Now this part I am getting a bit confused by because the lore contradicts you and you are really pushing your headcanon. Also, I am seeing a bit of redefinition here. Let's try to keep things objective as possible, we don't want to be intellectually dishonest
The citadel send the signal to the keepers, not the catalyst.
The citadel being part of the catalyst is something totally irrelevant.
Because the citadel is not the catalyst
The citadel (100% of it is part of the catalyst - how much of the catalyst is comprised by it we don't know) Sends a signal to the keepers
The citadel being part of the catalyst is something totally irrelevant? Huh? This is where your redefinition fallacy is coming through as well as a good amount of headcanon. Please show me how the citadel being part of the catalyst is totally irrelevant when we see it closing/opening the arms in ME3. And the fact that the reapers are a part of it too and we derive from the material that the catalyst controls them completely (we have no reason to doubt the catalyst).
The citadel is PART of the catalyst. To what degree the citadel makes up the catalyst is unknown. I think in your mind if the citadel comprises 100% of the catalyst then your argument looses and there is a continuity issue, however you are trying to leverage headcanon (and redefinition) to say that the citadel is NOT 100% of the catalyst therefore the keeepers will not respond to the catalyst.
However, the issue with this is the lore contradicts you - again. For one part, assuming you are correct how is the catalyst even able to open/close the arms, raise the platforms, etc in ME3? I thought the citadel was like a heart - you have no control over it? You can see where the false comparison breaks your argument both logically and relative to the lore. The second issue is that if we look at the reapers (also part of the catalyst) we see it controls them completely. From this we actually derive the following deductive statement:
Anything that is part of the catalyst is controlled by the catalyst
The Reapers are part of the catalyst
The Reapers are controlled by the catalyst
I really do think if I was to make this statement in another thread that we weren't having this discussion - you would raise no issues to it, that is just my opinion though. This is the second deductive statement that you will have issues with:
Anything that is part of the catalyst is controlled by the catalyst
The Citadel is part of the Catalyst
The Citadel is controlled by the Catalyst
Thirdly, even if we remove direct control (which seems to be heavily inferred) we have the keepers, responding to signals that are 100% coming from something that is part of the catalyst (and the reaper mastermind). If the reaper mastermind has part of it sending signals to the keepers, how could it not open the arms? I will tell you it was NOT the prothean sabotage. It was the writers potentially not peer reviewing their work - or just hoping people would just "go with it" IDK, I am not one of the writers so I can only speculate on intent. What I can do is look at what they write objectively and see how it interacts with previous parts of the narrative. Narrative Coherence - as we know - is the logical consistency of a narrative (or how logical and consistent a narrative stays to itself).
I love your gumption, but objectively, anyway you slice this is a continuity issue. In addition, you did explicitly state that we did not need headcanon to show there is no continuity issue, however looking at your posts you say we needed "logical interpretation" to "make it work" and you are using logical fallacies to back up your claim (thus tarnishing and breaking your statement about a logical approach as fallacies are not logical). You have, essentially, pulled a "mac walters" (broke your own continuity trying to defend the broken continuity of ME3)
In a way, it is actually kind of cool.
Here is what you need to win:
- a cut scene, codex entry, piece of dialog that shows how/why the catalyst couldn't open the arms in ME1 (taking the assumption that it was on the citadel in ME1 and - as we both know - not yet thought up by the writers). Not your interpretation.
And/Or
- A cut scene, codex entry, piece of dialog that shows how/why the keepers are not responding to the signals coming from the station that is part of the catalyst (and also is his home). Not your interpretation.
And/Or
- A cut scene, codex entry, piece of dialog that shows the catalyst was inactive in ME1. Not your interpretation.
Much work you must do young one 
are you human or are you a computer program? 
That point is an area of much contention with my coworkers. 