A transgender pupil will still have been primarily socialised up to that point within the gender that the school is aimed at. Therefore they will face the same potential issues as other pupils and (in theory) benefit to the same extent from the single sex education.
I used to be of the same opinion, but then I met a FtT, and changed my opinion. They can be exactly as overbearing as any male.
Don't you think that teachers who have subconscious biases against girls and want to dedicate more time to boys (as studies have observed to be the case in coed schools) would encourage the pupil they have been told and are forced and coerced to treat like an actual male by threat of losing their job more to excel at maths, and start to hold gender stereotypes against the other girls, because lo and behold, there now is a boy?
If they treated the transboy exactly the same as every other female pupil, wouldn't "he" feel that this "invalidates" his "gender identity"?
It's also about acceptance and tolerance, and making sure that teenagers are supported and not ostracised because of their personal identity.
All FtT I have talked to were, some more than the others, male supremacists. They wanted to be perceived as belonging to the "better" and "worthier" sex, it was apparent in the way they explained why they were trans identified (soooo different and sooo uninterested in that stupid femininity that we know all girls who don't believe in genderism totally love).
Their "personal identity" is an insult to girls and women. I just don't think it's fair to force girls to go to school with someone who feels so smugly superior to them.