Why do Mio and her friends seem to all wear different uniforms? Mio, who is a student at Reiji and Ellen's school, is introduced in episode 20. It quickly becomes apparent that Mio's friends all wear different uniforms. This is most obvious in ep. 22, where we see a photo of Mio with Sanae and Ellen, after which Hirono, Sanae, and Ellen appear.





Why do the female students not have a standardised uniform? I have never seen such an egregious case of this. Other examples of differing uniforms are much easier to explain, and none of the reasons there seem applicable to Phantom.


In Sailor Moon, Rei is a transfer student and wears her old school uniform. She claims to have been unable to find a new one in her size. No one else wears anything different.
In Kare Kano, students do not all wear the same cookie-cutter uniform, but it is explained in the manga that the school offers a variety of styles for students to wear. It is also very clear that ultimately, these uniform combinations can form a coherent image for the school. In contrast, it is hard to imagine that these girls' uniforms from Requiem for the Phantom come from the same school.
In Kill la Kill, everyone except for the student council and Ryuuko seem to wear the same uniform. The student council and Ryuuko have been set apart from the other students, so it is not unreasonable that they should dress differently.
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.