@EvelynIsGone:
I made that argument when the pertinent tags were being re-arranged, but IIRC, the admins felt that there were too few manga that actually talked about transgendered people, to merit a tag for it.
I am tempted to say that the tag should be removed in this case myself. It's an interesting question as to whether it's technically "correct" or not, as it stands, but regardless it seems a bit insensitive (though not as insensitive as the handful of cases where, for instance, a manga with female-identifying biologically-male character explicitly dealing with gender dysphoria, got labelled as "shounen-ai").
But I don't know. Removing all the gender-y tags from everything that treats the issue seriously, seems to conversely play into the idea that everything with "magic" fantasy/sci-fi gender-swaps are just fetish material, when some of them are using it to allegorically talk about many of the same gender issues... Or am I just overthinking things way too hard, here?