I can see what you mean by Pope Francis is actually undermining his own goal of making us believe there are real and important differences between male and female by putting down people who want to change their gender surgically because they feel that the opposite gender differences are ones they more comfortable with and this makes them feel they are in the wrong body of sorts.  If Pope Francis were to be willing to state there is no actual important difference other than the genders must have some physical differences to procreate then his critique of transgenders would be more sensible. His sexism makes him accidently more supportive of transgender's claim to have real reason to change their bodies. 

That being said I have asked transgenders and when they explain why they feel they were born in the wrong gendered body, their answers always go back to false stereotypes.  Such as I am a man but I am a nurturer and emotional and creative or . . . .