One thing I am confused by though, is that one the one hand it mentions that children (under 18s) cannot have Gender Reassignment; but it then goes on to say that if a school has a child with gender reassignment they have a protected characteristic so………
This is the difference between having a Gender Recognition Certificate (GRC) and having the protected characteristic of Gender Reassignment. The first is unavailable to children (Under 18s), but the latter can apply equally to children. IMO to legislation is so poorly worded that nearly anyone could claim to have the protected characteristic of gender reassignment.
That said, it is no different to anyone claiming to have the protected characteristic of religion or belief.
My understanding is that all either of those things mean is that you cannot be discriminated against because of your self declared status, not that you must be treated as actually having that status.
I don't have specific info/knowledge to hand on the HRT point but any medical treatment should be administered on a risk/benefit basis. So women (females) are granted HRT because the benefits outweigh the risks. For men, I can't see how that can be the case, unless the patient is arguing psychological 'harm' of not taking female hormones, which is a common TRA argument.