I think the term "transgendered," is an outdated insult really. It's trying to keep sex and gender linked, as if from the outset your gender has anything to do with your sex. The implication being that if transgender is to not have a gender that matches your sex then there must be some match between gender and sex in others. Obviously the two aren't linked at all. You shouldn't use the term, it's insensitive to the people you're trying to help.
But yeah as for boy/girl/man/woman being gender terms, that's what some people want them to be now. Good to let everyone know.
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I'm not offended by the term trangender. The one phrase I really hate is, "Tranny." It's extremely outdated, and is more often than not a derogatory term used belittle the trans community. Basically it tends to be better to inquire about a transperson's preferred pronoun, (him/her), and stick to it.