What if, hypothetically (I wouldn't want to get fired), the most qualified split was 55% male - 45% female. Wouldn't aiming for 50-50 be discriminatory towards males?

Since we have no way of knowing what the actual qualified split is, aiming at anything is discriminatory towards everyone.

She means that aiming to 50-50 doesn't represent the skills set. As women are more skilled for that job they should have more representation (based on the biological theory). If it is a 50-50 you are promoting men in the positions when you shouldn't. (the disadvantaged group here are the men)

You're missing my point. If women would naturally have more representation and were disadvantaged by this policy, and the policy was 100% effective (unheard of), their representation would drop from >50% to 50% - it wouldn't somehow switch to women being significantly underrepresented. This assertion doesn't make sense based on the actual situation we have today.

I don't know if I understand you. We have the situation we have today because "biases and unequal opportunities".

I think the person you're responding to is assuming that we are already at a decently fair equilibrium, and that diversity and other concepts and goals are disrupting that equilibrium. I think the biggest failure of communication around these issues is that a lot of people arguing against these programs are coming at it from the just world hypothesis.

https://en.wikipedia.org/wiki/Just-world_hypothesis