The difference is that we know that unjust discrimination and social pressure exist; we know it was historically very bad; and we have a concrete theory of causation. With the biological explanation there is no theory of causation.
But you claim we have no possible theory for how DNA could make men and women's minds different, or that society could create differences in how much genuine interest women have in tech?
We don't really know why some people are straight and some people are gay. Does this mean we deny that gay people exist? My father is gay and his identical twin is straight. How did this happen? According to Wikipedia, studies have shown this trend often enough to conclude that genetics alone can't explain sexuality. So do we just argue that there really is no difference between gay and straight people (ie. it's a choice), because we don't understand the precise reason for the difference?
Even if your description of the situation is accurate, just because there's a theory on one side and none on the other does not remotely imply that theory is automatically correct and should be acted upon.
For the people living in those historic eras. We don't know the effects it has on people living in the modern era.
And then you have to make the leap on why tech companies should be enacting social justice in the first place. They're not the guardians of society. Social justice is inflammatory and hiring is basically a zero sum game because "diversity" doesn't affect head count (other than for the liberal arts majors and recruiters who have made careers out of the diversity issue)