Which is the original version and the meaning. (As in coitus.)
The very term (sexual intercourse) implies a male-female connection. It is a modern shifting of the term to imply sexual intercourse as anything else.
The secondary definition in webster lists sex + sodomy as a definition for sex. Which would've made sex in texas illegal until recently and probably comes from the colloquial and legal 'sexual assault' addressed in a bit.
We could ramble on about this, but, yes... sex (classically and I think legally) means coitus.
However, many states have lumped together a bunch of things under "sexual assault" and this might be where the watering of the term comes from in modern usage.
Anyway, that's my two cents. I'm not a linguist.