I enjoyed this article a lot, it's great to see another huge fan of the early Resident Evil games. I don't buy a word of it, of course, but it's great to see theories like this and the Indoctrination Theory popping up.
Anyway, I'm too lazy to read the whole thread to see if anyone has already mentioned it, but just in case no one has; there's a small error in your article.
Ada's actions in the Leon B scenario - where she is wounded by the Birkin mutation but survives, and eventually aids Leon in killing the monster.
It's a minor mistake, but Ada isn't wounded by/doesn't assist in killing Birkin. You're thinking of the Tyrant (commonly called Mr. X, or That Pale Giant Guy in a Green Trenchcoat and Holy Shit It Just Smashed Right Through That Wall) that pursues a character throughout their B game, Nemesis-style.
Leon is fighting Captain Trenchcoat when Ada attempts to help and gets a sound beating and a choke-hold for her trouble. As Sir Trenchcoat is attempting to strangle her to death, Ada empties a clip into its face, and it falls over the edge of the balcony that they're fighting on, and into the pit of molten whatever below. Leon stops doing whatever it was that kept him busy while Ada was being murdered by Lord Trenchcoat and stops by to see if she's okay. Turns out she isn't. They kiss and she dies. Or so we're led to believe!
Later on, Leon encounters a certain pit of molten something-or-other, and out pops Dr. Trenchcoat, sans trenchcoat, plus giant claws. Leon fights it for a while, but can't kill it. But then someone appears - subtly implied to be Ada by virtue of looking exactly like Ada and speaking in Ada's voice - and tosses Leon a rocket launcher, before running away again, because running away from Leon worked out for her so many times in the past. For his part, Leon looks on and shouts "Ada!" as he is wont to do.
And that's it, pedantic and unnecessary correction complete.