I don't see why he can't get low dose T prescribed by his doc. This should remain confidential and there is no way the father of the kids can get evidence from his doc about what meds he is on ( at least I don't know how he could get at this confidential information which is totally unrelated to being able to care for children).
The T prescription will need to be very low dose or else the first give away will be lowering of his voice, and there goes him appearing female, at least he might still look female but his voice won't. All the more reason to encourage him to get T from his doc.
I hope he sorts out the custody. It can be awfully stressful.