I remember the plot like this: Boy meets an alien flower of sorts, I think, and is granted one wish, but his wish is to become a girl. The plot follows him becoming a girl. He was also in love with his best friend?? IIRC.

The mangaka, as I remember was at least at the time considered a woman (but it might have changed since X-gender came out since then) and was relatively well known for her other works, but this was a more minor, lesser known one.

The manga explores sexuality along with gender ID and I think it's a shorter series.

It was never made into an anime.

Uh sounds kinda like Kanojo ni Naru Hi (in love with male best friend, gender change, female mangaka) but I don't remember the alien flower bit (or mangaka gender spectrum) so might be something else

Sounds really close to Kashimashi - Girl Meets Girl , but this one does have an anime adaptation.
Could also be one of YOSHITOMI Akihito's works, sounds like something in his wheelhouse. Check out Blue Drop or one of it's off-shoots in particular. Though the second part of your post makes me think it might not be his work you're after.

I found it. It was https://www.mangaupdates.com/series/spd1eat/blue-wars by NAKAMURA Yoshiki

Thanks for your help, though.