Sometimes this series has a very weird way to say if its or not transfriendly or transphobic (for a reason Mino DONT change her gender to a girl again, dont know why)
it's neither friendly or phobic toward that topic.
it's looking at it realistically.
of course there is the important difference in this story, that people change genders against their will, having lived in a gender they (in this story at least) felt comfortable in.
changing into a gender like that, must be a level of horror that nobody can imagine.
and even if the surgery is an option, as has been spoken about in this manga, it's never going to bring you back to the way you were.
this is about losing one of the things that made you, you, and having no way to somehow get it back again.
these people change into the opposite sex 100%, their minds are affected, their thoughts are affected, their personalities are affected against their will.
i would never go and compare this to transgender.