I don't mean to be that guy but I think if Rin was an out and out transsexual then they'd have had an inner monologue about wanting to be a girl outright, not an inner monologue about wanting to wear a skirt. I think it's perfectly valid to have the stance of "ultimately I don't really care about being either a boy or a girl, but functionally being a girl is more conducive to the self-image I want to have that caters to my tastes," and I think that better describes Rin's feelings rather than calling them "trans" in the typical gender-identity sense.
The fact that they didn't really undergo a particularly drastic transformation also gels well with the idea they don't care all that much about the body aspect of it. If anything, the transformation was highly concentrated in the thighs, which would be the most relevant part of "showing off with a cute skirt."
Let me put it this way. You can want to be a girl because you care a whole whole whole lot about your sex, or you can want to be a girl because you don't really care that much about your sex, and I think Rin seems to fit more in the second category. If they grew up in a world that did not have skirts, I'm not sure they would sign up for witchification. That doesn't stop them from being properly "trans" pending further revelation, but I don't think it's basis to definitively call them that as of yet. It's important to not jump the gun and see what you want to see, rather than what is.
But that is simply my analysis.