But the story obviously wasn't referring to biological sex, but rather to the gender presented by the booth-worker. So "female" was also the incorrect term, besides being off-putting.

Yet is still a very small minority, and it appears that you are needlessly seeking out ways to be offended when no offense was meant.

Not sure what in my post indicated that I was offended. The cultural context of the industry might be apparent to you from within that context but not everyone who reads Hacker News lives in that same context. That biological sex and cultural gender are not the same is not something that is held to be true everywhere. Explaining the context we live in is not the same thing as being offended that some either don't understand or dislike that part of our culture. Or to put it another way, don't shoot the messenger.

I do not think that was the intended usage.

gender is not a theory.

'identifying' as another gender means wearing a stereotype.

Actually, gender is and was always a theory. Before it was applied to humans in the current sense, it was a grammatic theory. This idea of gender as another name for sex is simply ahistorical - seriously, just go to Google Books and search for "gender" before 1955. It's only about grammar. Then John Money came around and use the word exactly to draw a distinction between biological sex and the cultural/sociological construct.