Well, as for me, i don't like the idea of Schala-hime being merged with Kid. But i have different reasons. Mostly because i greatly dislike Kid as a character. Blond hair, blue eyes, stupid accent, much less brains than her prototype had...brrr...no magic (screw the element system!)...
I prefer the idea that Schala, seeing that her clone has become an independent person, just let her be and went off by herself. I don't think that she would like her head being filled with "Serge, i miss you! Serge, i'll find you!". To her Serge is nearly no one. Just the boy she saved (Everyone knows she is a caring person), just the tool to reach freedom (Well, she never planned it to that part...but still...Maybe she isn't much different from Janus and Zeal...manipulating everyone to reach her own goals)
Schala alternating between characters and also speaking as if she were with the party in the opening cutscene.
Emm...the opening cutscene is the first part of the final one, when Schala "Kid" Zeal closes the book she has been writing. That is not an evidence. You can use it to prove both versions.
P.S. sorry for some mistakes in my english. I'm not a native english-speaker.