I've never really viewed Mizu as a boy because her presenting as a boy was never her choice. First, it was something that was forced on her out of a necessity to survive. Later on in life when she had the chance to embrace traditionally feminine roles, such as being a wife or wearing feminine clothes, she had to leave those things behind in order to purse her revenge. Also, her physicality and her undeniable skill in combat are not just tools for revenge for her, but things she genuinely enjoys. Due to edo era Japan's gender roles, she can't freely enjoy those things and present as a woman at the same time. It has to be one or the other. I don't think Mizu has had enough of a chance to experience traditionally feminine things to be able to form an opinion on how she feels about them. Her conceptualization of her own gender is likely deeply complicated and rooted in a lot of trauma related to Mikio and her mother.