What I mean is what's the difference between 3099 EMS and 3100? Why does Shepard die in one and live(?) in the other? There is no clear reason besides "Because reason" How can one appreciate Shepard lives when by all indications Shepard should be dead.
I mean, I can't justify it by saying Shepard was able to take shelter, or shoot from a distance (we clearly see Shepard walking into the explosion just like every other Destroy ending) We can't say the explosion was less intense, it appears identical (and equally massive). We can't say anything, except "breath scene"
When you are dealing with someone else's character, especially whether said character lives or dies, you better be 100% clear why their last image of said character is a faceless torso and what that means exactly.
A couple of points here: The difference between 3,099 EMS and 3,100 EMS is that 3100 EMS is the cutoff point to get the breath scene. When you have a numerical system, it's inevitable that there will be an arbitrary cutoff point of this sort. Suppose there's a P/R check that requires 4,000 paragon points to make. Does the difference between 4,000 paragon points and 3,999 paragon points represent a substantial difference in terms of reputation or personal charisma? Not really. Nonetheless, you can make the check at 4,000, and can't at 3,999, because there has to be a cutoff point somewhere. Same with the breath scene.
The main reason why the last image of Shepard you see is that of a faceless torso is most likely that this required fewer resources; no matter what you did during character creation, that obscure part of the torso is going to look mostly the same. It wouldn't be the first time something like this happened in ME3 (Tali's face, masked Quarians during the consensus mission, etc.).
This is admittedly drifting a bit off topic, but I pretty much gave up on the idea that Shepard was 'mine' in any significant sense after the auto-alignment with Cerberus in ME2. The way I see it, Shepard is more like Adam Jensen from DX:HR (i.e. you can control some of his choices but a lot of his background, relationships and actions are pre-determined) than your average blank slate. I suspect it's a necessary trade-off when you actively pursue that kind of overtly cinematic style.
Since the "only life" rule is so irrational in the first place, I gave them a pass on that. Liquid metal is "alive" enough for the purpose of time travel, I guess. Since we don't know the mechanism, why not?
The "only organic material" rule may not make much sense, but it is necessary to explain why people from the future don't bring their phased plasma rifles in the 40 watt range or even clothes with them (it's also necessary to push the "time travel as birth" metaphor they've got going on). Also, I'm not sure what's meant by "alive enough"; that sounds a little bit like "pregnant enough." Regardless, I'm not sure we're actually in disagreement about the main point, which is that it isn't always necessary or even desirable to look for in-universe explanations of everything, or to radically re-interpret events when those explanations can't be found.
EDIT: Fixed wording.