a similar thing in The Faculty -- the goth-punk, rumored-to-be-a-lesbian girl is seen at the end, after she and her fellow-students defeat the alien infestation, wearing pastels and holding hands with a male student (who'd also helped defeat the aliens.)

I haven't seen The Faculty, but that sounds like something that would annoy me, yes.

I suspect Hollywood (Tim Burton excepted) uses Goth/Punk/Emo looks to signal that a character is bad/rebellious/unhappy, and therefore if they cease to be bad or unhappy, this must be signalled by "removing the disguise" and switching to the supposedly neutral state of mainstream dress.

I suspect you are correct. It would be nice sometime to see that subverted without the subversion being the entire point.