I have to say that you are pretty dead on with everything you have said Ieldra. I'm very impressed and in awe with your interpretation. I admire your dedication and the time you put into this, the amount of research that you have done.
The Synthesis ending is indeed the only ending that tackles all the themes of the game. Two of the main themes are "Synthetics and Organics" In this case it also covers the whole conflict and desire to understand each other. Much as you have stated. It goes from "Synthetics vs Organics" to "Synthetics and Organics". Another major theme of the game is unity. You spend a good majority of the game resolving conflicts. Racism is a huge sub-theme that resides under this subject. In the first Mass Effect you need to prove humanity's place in the galaxy. In the second game you're bringing people together to form a team. Unifying more personal relationships. In the third game your main goal is to unite the galaxy under a single banner to defeat the Reapers. In order to do this, differences must be resolved. Set differences aside. Much of the game you are doing just this. You repair the relationships of with the Geth should you do so. You solve a major conflict with the Quarian's, should you choose to do so. The Turian's and Humans set their differences aside and try to forget about the "first contact" war. You fight along side the Asari and gain their trust as you defend their home world. You bring the Krogan race together, solving their problems and see them cheer with the end results, resulting in peace for their species. If you play your cards right. You can see how obvious what the ending is. In order to unlock the synthesis ending, you need to amass a high level of EMS. In order to this, you must unite people together, build your numbers and your trust amongst your allies to stop the galactic threat. I could go into many more details, but it seems that you have already done so 
I just want to point out a few things;
While yes racism is a theme in Mass Effect; Organic vs synthetic as well as organic vs organic and even synthetic vs synthetic, and the "stand strong alone or strength through unity" was a theme in at least the first game, I don't think Synthesis addresses them well, if at all.
Sure resolving differences and getting people to work together is great, but doing so by forcing people to undergo physical changes? Forcing people to become something other than who or what they were? I find such implications unpleasant. Not to mention rather pessimistic of the state of humanity and the other races of the Mass Effect setting. Are they so flawed that they are unworthy of existence in their current state?
I also want to add a few things regarding the Synthesis ending. I want to point out something that isn't story related at all. It is related to basic game design and level design. Traditionally when you design a level for a game. You position the player to have a line of sight to the place you want them to go. One example of this is to place them in front of the destination. This is something the whole Mass Effect series does very well, even with their dialogue wheel (Paragon is often on top, and Renegade often on the bottom. There are some trick ones to mix it up.). In this particular case. BioWare positioned the player in a direct line of sight of the Synthesis ending. Then you have Destroy to the left and Control to the right. The player must "go out of the way" to get to those locations. This is often used to present optional areas in game design. While this isn't the case with all games. It is often almost always the case at the beginning of every level. The exception of the rule is no different on the Crucible. I will also point out that both Mass Effect 2 and Mass Effect 3 have very liner level designs. The player is given some choices on progression, but it is limited and remains linear. This is simple game design 101 logic.
I want to stay away from insults, however I must point out that there is the other endings contain zero rational reasoning. The logic is so flawed beyond any moral interpretation. In the destroy ending you continue the cycle naturally without the aid of the Reapers. The peace will not last and differences will inevitably resurface. This time the Mass Relays are destroyed and various races with different ideals and beliefs are stuck on planets together. So many different races are on Earth and the war will be unlike any other that has ever occurred on Earth before it. Many races residing on Earth will be wiped out, if not the whole planet should the Human's or Krogan's make another atomic/nuclear weapon. Let's not even go into the details of what the Turian's can cook up. The risk of peace and life itself will remain at an all time high. The control ending is very self-explanatory. I can go into a lot of details, but I will not. Understand that "absolute power, corrupts absolutely". The end results would be very nasty should your Shepard be a renegade. Only by becoming connected, individual, embracing love for each other, understanding each other unconditionally, can peace be achieved. There is no evidence that individualism is lost. There is evidence for understanding each other internally, each others points of view. As you said, it is the final stage of evolution. It is both transcendence and ascendance. "All is one". Yes, the Synthesis ending is very much a cosmic and "new age" philosophy.
I should also point out that throughout ME3, at least, the "line of sight" was always to destroy the Reapers. Even Shepard's Paragon response to the Rannoch Reaper states "I have a better idea: We destroy you, and live our lives in peace" Then there was the Cerberus plan to control the Reapers, though that was not gone into in depth so much. So from a storytelling viewpoint, Synthesis was never really in our line of sight as much as destroying the Reapers
Don't take this as me advocating the Destroy ending. I'm on record as being against all of Bioware's endings. I thought they were all terribly done. So don't take my picking apart Synthesis personally either 
On that note. I will also point out a major fact regarding the ending. BioWare will never publically announce a cannon ending. This is because the entire Mass Effect saga is your personal story. Therefore the ending is your story. You choose your ending and let you imagination run wild. For example, the indoctrination theory is false. It is true that there remains some content in the game from that cut ending. However, should one believe that ending, despite the mild evidence that remains in the foreshadowing stage. That is for them to believe and that is their ending. Even if it is not the correct ending that BioWare intended and is canologically wrong. It's your story. Is there an ending that BioWare considers to be canon internally? Perhaps there is 
I'd say if Bioware really cared about how we ended our Shepard's story, we'd have had very different endings. the crop they gave us is radioactive, even four years later. That, more than anything else is why they aren't going for a canon.