I mean, Nekomiya provides a total of two (2) front-facing possibilities: that she’s a cis girl fucking with you for kicks, or that she’s a trans girl fucking with you because she’s scared. The cross-dressing “option” is just solipsism on the part of the protagonist and misapprehension on the part of the author.
There are crossdressers/men in drag that aren't trans. Nekomiya's "backstory" (we dont even know if that's even true) can be interpreted as a closeted trans girl, but at the same time nothing refutes the possibility that it's really a he who just enjoys crossdressing. Freedom to wear what one likes has always been something some men wished for.
I’m not gonna say no crossdressing guy has ever had issues with body image because that’d be utterly unfair, but what crossdressers don’t experience is gender dysphoria as a result of how they’re pressured to present in the world. What Nekomiya describes in her original claim is absolutely a “trans narrative”, only furthered by the protagonist’s “I don’t date dudes” dismissal and grotesque obsession with her genitals.
Again, she may be cis, but nothing she says in the manga suggests boyhood (I understand the author is trying for that gender confusion schtick, but honestly fuck the author).