What does a confounding variable have to do with anything here?
The question is "do women make lower wages than men"?
You are adding confounding variables I assume because you are uncomfortable with the fact that the answer is "yes", but are less uncomfortable if there's some reason that it's yes other than "people deliberately pay women less".
Of course there are reasons women make lower wages than men. That doesn't really matter, though: if the gap is itself a problem as an outcome, the fix is very simple, and the reasons don't particularly matter.
If I asked which of the two of us is taller, all that takes is a measuring tape. The fact that one of us might have gotten better nutrition as a child, while possibly interesting, doesn't actually do much about the fact that one of us is really taller than the other.
