Oh boy, modern politics and ideology in manga, that can't go wrong at all. I wonder if the author is ignorant or an idealogue. The androgynous children & wording of this chapter could lead me to the latter. Or perhaps it was nuance lost in translation. I really hope this shit doesn't get ratcheted up and ruin one of my favorite series.
Being raised as the opposite sex isn't what gender dysphoria is, nor is behaving like a tomboy or tomgirl(?). Gender Dysphoria is an inborn mental illness. Being raised as the opposite sex is something else entirely. They aren't mutually exclusive but I doubt this is a case where they're overlapping.
As far as I can tell, this doesn't seem like genuine gender dysphoria, especially since she's a kid and what's often mistaken for gender dysphoria in children is outgrown once the child reaches adulthood and she was specifically raised as the opposite sex, and did not coming to that conclusion on her own. Being gay and or a tomboy and or confused due to upbringing seem far more likely than genuine gender dysphoria.