In Some Like it Hot two guys, played by Tony Curtis and Jack Lemmon, are pretending to be women. Everyone in the audience knows they are not really women, and part of the joke is deciding how well or badly they have managed it.
That is also Julie Andrews' motive in Victor Victoria. We didn't buy her either.
But if you didn't read about it in advance, you might not have known that the male character Billy Kwan in The Year of Living Dangerously was played by a woman, Linda Hunt, currently of NCIS Los Angeles. I suppose this is the only case I can think of that parallels operatic cross-dressing. The singer in an opera is supposed to be the other gender and not just pretending to be.
I especially loved this movie because of the scene where the older man (Linda) introduces the younger man (Mel Gibson) to the joys of the Strauss Four Last Songs. I believe if memory serves, that the version was Kiri te Kanawa.
The Crying Game was a special case. Everyone I knew did a fabulous job of keeping the secret that Dil was actually a guy. If you knew, it spoiled the joke. He takes a man home with him and we get to find out together with the man on the screen that his plumbing is not really female.
This is based on an item in Entertainment Weekly. I used different pictures, but the idea is the same. No one thinks anything of cross-dressing when it's a joke.