There are stalls in locker rooms, you know. It would be no difficult task to retrofit showers to hide the body. People can wrap towels around their wastes or the entire body. Come on. This is not difficult.
Most trans* women are also very much ashamed of their anatomy before transition. They would not want a bunch of other women to see what they do not want them to see. It would make them far more uncomfortable than what the other ladies would experience.
Puberty is an awkward time for everyone, but I do not find it very compelling to restrict the existence of co-ed bathrooms on the basis that someone may find someone else’s nakedness disturbing. There are some cis-women who develop over-sized clitorises which could become erect like a man’s. They were locked away in asylums for nymphomania, among other things, once upon a time. I am sure they, along with some intersex folks, are still given the business for what they cannot control.
But I do find the idea of private bathrooms and locker rooms for transgender students to not be a deal breaker. However, those would also have to be separated into two different compartments in keeping with your position on co-ed bathrooms and locker rooms. I seriously doubt any school would construct four separate facilities in key areas of the school for their students.
The whole idea of separate bathrooms was not even a scientific one. It was based on “separate spheres” nonsense from the Victorian Era because men did not know how to deal with women in the workplace. The premise behind it was just as laughable then as it is now.
So while I understand where you are coming from, I do not entirely agree your solution to the problem is the only one realistically available.