Isn’t the soul that is baptized? This is what happens when you continually change your doctrine to suit the times instead of trying to lead souls to heaven. Sad.
It’s the “person” who is baptized. Since human beings, unlike angels, are, by God’s will, composite beings, that comprises soul and body.
That bring said, since reassignment surgery, wrongly so called, is a form of sexual mutilation, forbidden by both Divine and Natural Law.