Duplo, transwomen are born male, not female.
For a transwoman to have committed rape, they must still have a penis - indeed, many transwomen have no intention of having GRS, and enjoy calling their penis a "lady penis".
So if you wouldn't put a male rapist in with the women, then you wouldn't put a transwoman convicted of rape in with the women.
We have separate men and women's prisons for very good reasons. We segregate by sex in places like prisons, for very good reasons.