Yes, there could be other discrimination (e.g. there probably is some discrimination against women achieving high management positions) (although it's really hard to measure) - I agree that's a problem and needs to be solved, but it doesn't appear to me that the public discourse revolves around it (it usually ends at the "70 cents to the dollar" myth), and I think the current tactics are actually counter-productive (e.g. they're making men afraid of working with women, lest they say something inappropriate or wear the wrong t-shirt).
Consider a resource A. All humans should have equal access to this resource, but because of various social, cultural, economic and historical factors, minority groups B and C have less access to A than the rest of humankind. I don't think there is anything wrong with targeting those specific groups to help them engineer better access to resource A.
That's simply not the world I see myself living in; to quote Margret Thatcher, "The trouble with socialism is that eventually you run out of other people's money".
And for today's object lesson on that, see Venezuela, where those that are not pure money problems are inherent and unavoidable in the political process you're endorsing to "target a specific population". As shown by the very word target; in the case of Venezuela, replacing competent STEM types with politically reliable ones, 18,000 in the first wack, and then favoring current production over longer term investment necessary to maintain production levels.
Yes those it's unfair those 4 people take advantage of welfare, but for me, that's an acceptable cost for helping the other 8 who need it. I'm happy my tax dollars go to that.
Of course you can argue forever about whether the cost is worth the benefit, and whether basic income is better than welfare in this form and yadda yadda, but I'm trying to illustrate to you that in a system designed to help a population (I don't agree with you that women are not disadvantaged, but substitute them with any other minority group like black people), some people will inevitably abuse the system, but that's okay as long as there are enough people who benefit to justify the cost of the small number of abuses. In sum: helping a population with less access to resource A is not bigoted and, if implemented right, is a very reasonable approach.
Also there's nothing bigoted about folks working to make sure women get the same wages as men, or to break the cycle of poverty black folks in Chicago's south side are stuck in. Those are problems plain and simple, and they need to be solved.