Some of it had to be changed. I was told it had to do with text timings for the hack.
I know for sure the giant moo cutscene has some different text because I later compared it and asked about it.
Also the gamefaqs translation is an edit of the original it's self. I hope that if the game does get another chance at a translation patch that maybe some more revisions can be done with the story text in it's current state.