The sense of strong male and female divisions in regards to feminine and masculine characteristics in Japanese society itself are not so clearly defined as we might imagine them to be in the West.
They haven't been clear about this for centuries. Since, homosexuality is not an "out of closet" experience there like it is in the West, and very little, if at all, gay bashing going on, it goes without saying that discrimination for effeminate behavior, dress, and mannerisms is pretty much a non-issue.
Homosexuality is looked upon more as an anomaly, than as an "evil" as we have in Christian based societies. Guys would not have to worry about showing their "feminine-sides" in Japan. Guys cry there and express their feelings in an emotional way that would shock most Western men that are taught that "boys don't cry". Well, not in the USA they don't, but in Japan, just let a team lose a baseball game, and you'll see quite a lot of "blubbering" going on.
Men since the days of the Samurai warrior that are considered to be some of the most fearless, ruthless, and cold-blooded killers in history were still very much the androgynous/gender-benders.
And some coveted the love of young men, rather than women. They paid very close attention to their appearances, make-up, hair, nails, and clothing. It was always considered the samurai duty to die looking beautiful and smelling good, beheaded or cut-down into pieces as they may.
In all of this they didn't consider themselves homosexuals, in the same sense as Westerners take hold of it as a battle over heaven and hell, right or wrong, etc, etc.
http://www.amazon.com/gp/reader/0757000266/ref=sib_dp_pt/002-6124052-1906461#reader-link
There is still a large segment of Japanese young men today that are very much into high-fashion, dieting, clean-cut looks, etc. You have fashion magazines such as BIDAN (literally meaning "beautiful man")
http://www.fujisan.co.jp/Product/2199/
These magazines are popular for men wanting to "dress up" from head to toe, eye-lash to eye-brow, and make-up and skin care included, and this is a very mainstream publication. You have just as many men that are not into it either, but there is no great treatment towards either path.
There are such places to go as "TBC" for men,
http://www.tbc.co.jp/
which are totally aesthetic salons that cater to clients/ men to beautify themselves. Advertised by famous actors, and sports figures, both Japanese and foreign.
There is no homophobic stigma attached to these things. It is simply a choice.
The homophobic leanings that seem to be attached to these "girlie-men" type places for heterosexual men and women in the USA, simply don't register with the same scale in Japan.
Crossover characters in Anime I think are just another reflection on the fluid-like gender composition creations that make up the society there.