I would absolutely be going ballistic at the school here OP.
My children have friends identifying as trans. I am happy to be respectful, using preferred pronouns and names. I think trans rights are incredibly important but one vulnerable group's rights do not trump another vulnerable group's rights.
For teenagers I think this is even more important, because they are still developing their sense of self and identity, regardless of the absolute minefield of gender identity which seems under constant discussion. I will probably be flamed for this, but to me the number of teenagers identifying as trans and questioning their physical sex seems to be disproportionately high in this age group. I really worry about this for two reasons-1) Are vulnerable teenagers feeling pressurised into questioning their gender because of this and 2) There seems to be no way to safely encourage teenagers to critically examine their feelings over this, without being labelled transphobic.
I am not transphobic. There is no but there.
What the school has done here though is create at best an uncomfortable and at worst an unsafe situation for both the biological females and the trans student.
Teenagers are generally known for being embarassed undressing in front of others (PE flashbacks for me there, we had communal showers :/); this would be much worse I imagine if sharing a room with a trans person with the genitals of the opposite biological sex to yourself.
I imagine it would be equally mortifying for the trans person, as if you truly identify as female and know you have male genitalia, how would putting you in a situation making you visually confront the physical differences of the gender you identify as help you in any possible way?
I would be making both of these points to the school. In an attempt to be inclusive, they have put both children at risk physically and psychologically. A single room is realistically the only fair solution.
If we were talking about adults, and a fully transitioned trans woman I would feel very differently.