I actually have a genderfluid friend who specifically asks that people use "man" and "woman" to refer to gender and "male" and "female" to refer to sex. So a trans-man would still be a biological female and it would be fine to refer to him as such, as his biology is still that of a female human. But you'd call him a man.
This also helps for non-binary people who don't feel any attachment to being a man OR a woman.
After reading your post 3 times, I've still got trouble getting what you're saying. I'm a cisgendered male. Does that make me a man as my gender and male as my sex? Honestly, I find that a bit callous towards transpeople even though, granted, I don't know many but the few I know would take it badly if I referred to them by their birth gender. But please, explain because I feel I've misinterpreted something and I'm genuinely curious.
Yeah, you're a man and a male. Gender and sex are entirely different things; someone who is a trans man is likely to still be biologically female, which is extremely important for considerations like medical emergencies. Referring to a transsexual person as their desired gender doesn't change their biological sex, and even in 2014 we don't have the ability to 100% change biological sex from one binary to another.
It also allows for clarification regarding, say, sexual attraction. I'm predominately attracted to females. Not simply "women", but also females who don't necessarily identify as a girl.