Japanese media doesn't really pay much attention to trans as a whole.
Categorizing it wouldn't be that difficult. Any mention of crossdressing or traps can be under crossdressing, any conflicts of gender/transformation can be categorized as genderbend as well. Not like they have to be exclusive.
In the case of 'My Wife is a Man,' Kou never refers to his wife as a woman, and Yukio never refers to himself as a woman. It's a clear case of just being about crossdressing.
I would've thought it's common sense that the tags should be representative of the work as a whole but I guess that's not as common as I would like to think.I think a part of the issue is how users are tagging some manga. Some people add the tag to manga that has little to do with gender bender. Like in one chapter a character cross dresses and suddenly it gets a gender bender tag.