Women can wear pants now without people getting up in arms but it wasn't always that way. For a woman to wear pants was down right scandalous back in the day just as much so as men in skirts is today. I don't think gender and personal style have (or should have) anything to do with each other. I think one should be allowed to dress in the clothes they like not the clothes stereotyped to their gender.
And yes, Mana does still dress the way he wants to off stage. I refuse to say he dresses as a woman because I don't think that's fair. If you see a woman in pants, with no makeup, and short hair do you call her a "guy" or say she's "dressing as a guy"? Not typically no, although the phrase "Tom Boy" is still used a lot and in the aforementioned phrases' stead (which, again, I think is unfair). I think it's inequitable that women are allowed more freedom in their fashion sense then men.
You will also find that in Japan gender stereotyping, although it does happen (Oh, LORD, does it!), is very different then in other places of the world.