Now that I've Re-read it from the contest ch. I'm pretty certain Nagisa is a female, not a trans, just your regular female human being.
Now I'm kinda curious, how is the author gonna explain why the MC thought that Nagisa was a guy in the first place, just because she didn't wear a skirt while being on her duty? That's kinda lame of a reason, considering he's a crossdresser himself, that should've taught him not to judge people by their appearances. It's pretty obvious tbh.