At least in Batoto's and Baka Manga's tradition, gender bender never necessarily meant anything explicitly gender-identity-related, and has been an umbrella term for pretty much anything messing with genders or the concept of genders beyond the "that dude looks kind of like a girl" (or vice versa) level.
I assume some people get upset in a low-key way because of years of fighting transvestite/transsexual conflations, but in manga it's not always obvious which is which (and you can't really go ask the characters to clarify), so an umbrella term is actually quite prudent, I think...