I would think concerns might be over potential bullying and student interaction. Were not talking about adult students here that stand more to reason. It's a bit shocking to note this person is only 13 years old. A minor. It seems a bit early imo for a very young person to undergo something like this. Hopefully a decision not to be regretted later on but then again im not this childs parent.
Normally I would diss the school, but I would think this situation needs special preparations made prior to ensure proper accessibility and fair treatment involving all concerned. Im against denial to any student that is none of the schools business, yet there are assurances that need to be determined in light of the childs and peers ages and level of maturity. Im guessing thats what the school is trying to do but is having difficulty in figuring how to go about it.
All sai, it would be prudent to allow this person to attend as a female and address issues if and when they crop up and educate other students on transexulity. Im sure at this early age, a transgender person is somewhat rare and sensitive, especially at the level of maturity concerning other students.
Hoping an amicable solution arises that is fair and safe.