[baronchar]

I'm not from Japan, so I can't claim to be an expert; but I did read a book called "Wearing Ideology" a few years ago that addressed the subject of school uniforms in Japan. The author surveyed students and teachers from around the country.
I recall two things from it that may help answer your question. Firstly, a fair number of students actually like their uniforms and even choose to wear them outside of school as a fashion statement. And secondly, since some students do try to "customize" their uniform or appearance by altering it or accessorizing, some schools and teachers do give in to a certain extent.
I'm sure if there were goth-loli girls walking around the halls decked out in a full outfit they'd put a stop to that, but something like "loose socks" or brown hair might sneak by. It probably depends on the individual school.