For men who genuinely have the wish to become a woman, I have news for you, most men don't want that. Wanting to become a woman is a very deeply trans woman thing. If the protagonist wanted to become a woman, that makes them a trans woman. Even if they never came out or transitioned. Just like how a bisexual person is still bisexual, even if they only ever act on the straight attraction.
It depends what you mean by genuine wish. There's so much wiggling room for GB in between the male-gazey and self-aware trans stuff. There's a point at which strict boxes aren't very helpful, and the issue is more about bad actors and dishonorable pervs. Testing as 100% stereotypical cis or 100% straight-leaning or 100% homesexual-leaning isn't the norm, but unless it's an argument for empathy and civil rights I think it's often rude to type someone as bi or trans outside loose guidelines. I'm sick of heated hatefests about who deserves to be called lesbian and what era we should take the definition from. ...But with how hormones affect sexuality for some, it would be realistic for more genderswap characters to become bi.
A lot of people just aren't deeply attached to the gender they live. They fall into a cis box but a temporary or even a permanent change wouldn't phase them much. A button or cyborg body to change sex could be fun every other day or a decade, or they could be fine flipping a coin for the binary forever if given a meager incentive. Posthumans in The Culture novels change sexes at will once in a while without "trans" being a distinction. I Became The Daughter Of A Dragon is on point for the MC becoming more feminine while keeping pre-transition friends and aquaintances, adapting to and appreciating gender expression, but they'd be fine with a new start in life either way. One of the pair in Two As One Princesses is very much a girl, and transitioned over time in a way, yet recognizes gender didn't mean much to her before. I try to see most GB like this when it's not blatant ecchi fraud.
wait I can t remember a single one isekai that threat the dysphoria aspect, it is already rare that it is even a thing but in isekai I do not remember one maybe I am miss remembering.
if you remember the sone title that do threat it could you please give me their title
The most trans-focused GB isekai story I've read is
I Didn't Ask To Be The Demon Queen and its mirror novel. It makes the argument that for brain reasons a lot of people would feel crushing dysphoria after body swapping. MC is a dolt who lucked out. I'd seen comments that the upbeat professor MC in
I Quit The Hero's Party is eventually described as having found her previous body uncomfortable. I can't confirm it; the manhwa isn't far and official novel translation is expensive. I'm sure there are more that reference past dysphoria but that's all I can think of within the isekai/portal genre. Plenty more that you could read into their personality changes. It's more of an English-language thing to outright bring it up.