I really don't think a lot of traditional ideas of gender apply to Yukio, considering he grew up turning into a girl every day. I think that's part of why he's such a lovable character -- he's too innocent and blithe of spirit to be seen as experienced at being a girl, but he's too adorable and feminine to really feel like a guy. And it is telling how OK Yukio is with being a girl for good if it came to that. This is actually a very odd entry in the gender bender genre because it's hard to classify Yukio's gender identity considering their life circumstances.
To quote Tygan from XCOM 2: "Truly, I could not have predicted this outcome, though it is intriguing."
Ironically unlike one of the other commenters, I'd be very interested in a chapter or even a small arc where Amano begins turning into a girl. Just to explore how the two would interact. Even if it turned out to just be a dream or something. Or to just get some traditional gender bender flavor out of this. Barring that I am just happy being around Yukio and this manga provides that opportunity!