I think part of it is that it's a wish fulfilment of sorts for the audience; they don't get to deviate from their uniform in reality, but their favourite manga characters can. Besides, uniforms actually being uniform does not make for especially interesting visuals.
In any case, it's still within the realms of possibility. Length aside, the girls have the same skirt. Socks and shoes are often subject to guidelines rather than narrow rules. Girls having the choice of ribbon or tie is common, and they are the same pattern. Having different options for jumpers isn't too uncommon, and the designs available to boys are usually different to those available to girls.