They look so different with the regular uniform. And I'd like to know why they're pretty much the only girls wearing different clothes in that school.

It's because they're hip youngsters.

All the main characters have some difference with their clothing while at school, though I'm not sure if there are any other girls wearing thighhighs like Rise. She also has a white top under the black uniform, which I'm not sure if the other normal girls have (Chie and Yukiko don't have it above, but that could be the fan artist's error perhaps).

the only requirements seem to be the top layer and skirt for the winter uniform, i see a lot of girls with a different blouse underneath or with a jacket like chie's on