yuri really is just light hair girl x dark hair girl
It's just an artifact of how anime/manga art styles visually differentiate characters. If you can't reliably differentiate characters by their outfits because everyone's wearing uniforms, then all you've really got are face, hair, height, and proportions. Height and proportions have immediate consequences for how these characters are perceived by society, so the only two you can freely tweak are face and hair. So you're naturally going to give your leads significantly different hair colors to capitalize on one of your few options for making sure the audience can tell them apart, which is going to tend to result in one of them having significantly brighter hair than the other. Doubly so in manga where most panels are grayscale, or in the rare story with realistic hair colors.