All the conservative Catholic arguments against it tend to be conflate it with homosexuality or think that it's a problem of child rearing or whatever. However, they also tend to either ignore or be ignorant of the array of intersex conditions that exist, which are wholly biological conditions. They seem to ignore that there are congenital sex defects in general, which I don't understand. Either way, it's not much of an issue in the Church at this moment. I do know of an intersex woman who is joining a religious order, though.
Overall, these conditions aren't something that have been factored into Catholic thought at all, really. Probably because they're so rare. This is an issue for me because of the matter of my baptismal record and whether I can have a sacramental marriage with a female.