I don't know where it is that this happens. In gym class we would change, but never showered or got down to more than underwear, and that was over 30 years ago.
In any case, it's at the direction of the child and parents and what they feel most comfortable with. This has to be taken carefully and with forethought. It's a real tough choice. And in any case I think we as a society worry too much about "which parts". That they're hidden makes them forbidden fruit to some degree. I remember as far as the movie Robocop in 1987 showed a coed locker room where nobody particularly cared.
Here's the actual guidance letter:
http://www2.ed.gov/about/offices/list/ocr/letters/colleague-201605-title-ix-transgender.pdf
And on this specific topic:
- Restrooms and Locker Rooms. A school may provide separate facilities on the basis of sex, but must allow transgender students access to such facilities consistent with their gender identity. A school may not require transgender students to use facilities inconsistent with their gender identity or to use individual-user facilities when other students are not required to do so. A school may, however, make individual-user options available to all students who voluntarily seek additional privacy.