[ok...i'm going to try and explain this]
-rahxephon changed b/c ayato changed, think of it like an upgrade.
-the other doll that he fought was quon (ur talking about the end of the movie right?).
-and the reason why the one girl died when rahxephon killed the doll, is b/c her and the doll were linked, just like ayato to rahxephon.
[get it?]