This makes my blood run cold. So he probably did rape her with his penis but because he's decided that he is a woman, therefore, by law, he can't be charged with rape.
The law is clear that the offence of rape is committed with a penis.
Whatever the identity of the person to which that penis is attached.
A charge of assault by penetration means something other than a penis - an object or other body part - was used.
Which is still horrific for the victim.
And as has been pointed out already, the sex of the victim in this case is not stated. Either sex can be victims of rape or assault by penetration.