Speaking as a trans woman living in the US, I basically just chalk it up to it being a cultural thing too. Idk much about Japanese trans culture, so I try not to read too much into it, and not take it personally when a trans manga character refers to themself as "not a real woman/man"
As a trans woman myself, I can confirm gender dysphoria can be weird like that. Some trans people claim to have never felt it. I felt it in waves growing up. Sometimes it'd be almost nonexistent, then I would notice some new detail about my body (especially during puberty) that would make the...