I'm glad to see people posting openly about this! I've been on this forum since I was a teenager, and back then wanted to ask this sort of question. It's pretty typical that 'gender-bendy' individuals (for lack of a better word) inspire curiosity about their gender and sexuality. I find the curiosity to be understandable, certainly!
With regards to Mana's sexuality, I speculated about it as a teenager quite a bit because I found it to be personally encouraging to myself to imagine that he might be somehow, in some way, different. Of course, I was young and gay, and projecting my own feelings regarding myself onto him (I was in search for an idol to 'look up to'). The fact that I was projecting proves nothing in any direction about Mana's sexuality, and is solely a remark on my childhood perspectives as an individual. Anyway, now that I'm an adult, I think differently. I'm not projecting and closeted anymore, and am quite happy!! These days I think to myself, with regards to Mana's sexuality, 'I'll never know, we'll never know'. He could be anything. He legitimately could be straight, and I don't say that to 'be fair', I say that because it's entirely possible. Alternatively, he could be some other sexuality as well, and I remind myself to keep in mind the politics surrounding homosexuality and such in Japan throughout the time span of Mana's life, during the present day, etc. Or maybe, even, Mana doesn't ascribe to a specific label or concrete, succinct sexuality at all. This seems to be a real possiblity. Those doll remarks of his are particularly intriguing when it comes to that. All we know for certain though is that we're outsiders to a very private person's life. I for one, somehow???, have grown to enjoy the mystery of it all. At this point in my life, I prefer ambiguity to a definitive answer. I'm not sure why, hahaha, but I genuinely enjoy it! He's very interesting that way.
Now as for Mana's gender, I do know Mana has spoken about that! Perhaps this can help with your original question, OP? Here's the quote that I'm thinking about:
"It's absolutely not the case that I want to become a woman...it's a matter of personality...although I was born a man and am recognized by society as a man...I know there is also a woman inside me who transcends the time (jidai wo koete)...and I want to recognize the woman that is also inside of me"
Funnily enough, this English translation of Mana's quote is from a book on male homosexuality in Japan (Male Homosexuality in Modern Japan: Cultural Myths and Social Realities). The chapter the quote is from pertains more to the women's media discourse on homosexuality and the 'beautiful men' ideal. The quote was translated into English by the author, not by myself. The quote is cited as being from a March 1999 Da Vinchi article. The author also mentions that in the same article Mana remarked on "his interest in Virginia Woolf's novel Orlando about an Elizabethan courtier who changes gender as s/he passes through time." So yeah, hope this illuminates some of this gender stuff for you, OP! Sounds as if the way Mana chose to express himself publicly at that point in time is: he doesn't ascribe to a transgender identity, that he doesn't distance himself from being born a man, and that he has a very interesting and personal perspective of his ~ womanly side ~. So interesting how he puts it as a 'matter of personality', and a woman inside him. I'd like to invoke sanctum's thoughtful comment about Mana the private individual and Mana the public persona here, though. That's always something to keep in mind.
Also, I can't believe I'm on Scape posting about Mana's sexuality and gender on Christmas. I say this with no sarcasm or mockery-- what a world! Good stuff!