I never understood why so many guys have hangups about whether or not they're adjacent to being "gay". Constantly worrying about your level of heterosexuality and whether your manhood levels are sufficient sounds like no way to live. Not happily, in any case. (it seems to me that the men who win the chad race are the ones who didn't even realize they were competing)
In this case, Kakeru is clearly a woman now and is permanently so. He's attracted to a woman. There is little practical difference between Kakeru being a boy who grew into a woman and a tomboy who went more femme post-puberty.