It seems strange that a man would be allowed to daven on the woman’s side, but I’ll take your word for it; I don’t have access to the sefer you mentioned.
I would imagine that if such a person made teshuvah, the advice would be for them to get a haircut, lose the dress, and start identifying as a man again even if the surgical aspects are irreversible. If he’s still halachically a guy, then I’m not sure why he would be advised to continue dressing as a woman and sitting on the woman’s side. If we’re talking about a person who is unrepentant and wants to continue identifying as the falsified gender, then I think the question is best answered by N0mesorah’s TCT teshuvah above.