Alright (*whew* I can't believe I read that whole thing!), so let me start out by saying, I learned a TON about the theory of alchemy just now, but this did not tell me anything useful about Pokemon at all.
I have read alchemy books before and have even a small collection of some alchemy books as well, but I just really can't see any truly deep connections or secrets of it relating to pokemon. Sure I can get on board with the idea that the most basic and simple alchemy concepts that any kid could learn by watching something like "Full Metal Alchemist", might possibly be as some small plot devices within the game, but I really don't think it goes any deeper than the normal exaggerated fantasy concepts that pokemon often like to run in their games.
I highly doubt that there is any truly substantial alchemical secrets hidden deep within the pokemon games, and trying to over analyze it in this fashion will most likely just frustrate you with more questions than answers as well as most of the questions between pokemon and Alchemy you will encounter will cause you to ask why they're inaccurate or so vastly different between Alchemical theory, and the most common answer will be, "...because it's a fantasy game about pokemon."
I will admit, I love the fact that you spent so much time writing up this well presented synopsis of the basis for alchemy and it's overall theory, but I think trying to present it with pokemon logic is a fruitless endeavor that just adds more confusion to not only speculation of the new games, but it also makes the overall alchemical theory even harder to believe let alone interpret.
I do not think that the summation of the pokemon franchise is all built around Alchemical Theory, and I do not think that the Legendary pokemon you are mentioning were fabricated as designs of the varying elements and processes within alchemy. As a person who is fascinated by alchemy and has done a "decent" amount of study on it, I can definitely say that, although it is possible that these games might have varying alchemy influences, I highly doubt that it goes as deep as what you and other Alchemy fans have been implying.
It's really a cool well thought out theory, but I doubt it will go this deep, it's way too complicated, spiritual, and dark for a pokemon game.