Well... I have yet to see a school where students can change gender on the fly...
j/k
As far as I know, not all schools in Japan are draconian about the no-makeup rule. If it's not anything too flashy, I think the students can get away with it. Teachers can be lenient and look the other way if they can. In the context of the manga, wearing makeup is essential to a girl's life, so it's not too strange that a teacher (I think she's also a researcher), entices these special students to wear makeup. It's not like they were wearing flashy makeup, either.