@Smileyguy:
Boku Girl was quick to show the protagonist being a girl as better for everyone. Mizuki becoming male again even temporarily was to show they wanted to be a girl instead of accepting they had to be a one, and that being female was not the be-all and end-all of Mizuki's feelings for Takeru. (Also, it's seinen, not shonen, but that's besides the point.)
While
Ayakashi Triangle has emphasized upsides to Matsuri's transformation (realizing he loved Suzu, making actual friends), they're not really tied to
staying female. Recent chapters have even shown Matsuri growing
less tolerant of his situation. That's not really proof he'll become male again (it could even make it more impactful if he decided otherwise), but it's certainly not obvious he'll stay female in the end.
As for Soga/Matsuri, I see a
high chance of Matsuri ultimately staying faithful to Suzu, but still reciprocating some feelings for Soga. I don't consider that "bait", because I view a romance as having value beyond the couple being together in the end, or convincing the audience they might. And it's not like there's some huge resistance to it; I've looked at a bunch of posts about the series in Japan, and Soga/Matsuri is a quite popular ship.