Why do Mio and her friends seem to all wear different uniforms?
The school may have different uniforms for each class. This seems rather unlikely for the same reason you ruled out reason 2. In Tari Tari for example the girls in the music program have a dress while the other girls have skirt and shirt and tie. 

It is possible that the school doesn't mandate a uniform but the girls decide to wear something uniform-like anyway because wearing a uniform at highschool is part of the culture. Out of universe it also helps establish that the setting has moved to japan.