I just fail to see a meaningful connection between a deliberate action that comes with a plethora of emotional and psychological foundations, and a magical story device thrust upon a character by pure chance that more often than not comes with none of said foundations.
Magic/supernatural stuff is very often used as a metaphor for real-life issues, such as in Buffy the Vampire Slayer, where (as just one example) the magic curse that turns Angel into Angelus is a metaphor for the very common teenage girl experience of "my boyfriend suddenly became a jerk after we had sex." Obviously genderbending and transitioning aren't exactly the same, but they are very similar, and so to declare any comparison between the two inherently off-limits is very strange to me.
I would actually be interested to see a genderbending manga that discusses and uses the similarity between its concept and the experiences of trans people. So far I have not read a single one which did that, thus the claim that "many" do it seems dubious at best from my perspective.
Aside from the aforementioned Ore Ga Watashi Ni Naru Made (which might even have a literal trans character), there's multiple genderbending manga where the MC is revealed to have had dysphoria all along, including Kashimashi Girl Meets Girl and this one.
And the reason we have to resort to pretending in your example is because the manga does not address the issue of gender identity at all.
Everyone has a gender identity. The fact that Takkun completely accepts her new gender -- with her main concern being that her girlfriend won't want to stay with her -- implies that she sees herself as a woman. That's not pretending, it's in the text. The speculation lies in whether her condition changed her gender identity too, or if she was comfortable with (or even preferred) being a woman from the beginning.