Back when I first transitioned, I remember seeing stories about people who stayed in their relationships after they came out, even if their partner isn’t attracted to other members of their gender identity. My conclusion was that there must be a distinct difference between being attracted to a certain gender/type, and actually forming a romantic connection. Love isn’t conditional on being able to like everything about a person, but rather liking them despite the things about them you don’t like or care for.
What I am wondering is if Kanata falling in love with Yui has anything to do with whether or not she is a woman. Rather, I think Kanata loves the way Yui treats her more than anything else. If so, that might explain why she doesn’t consider herself a lesbian.