The person you're responding to went out of their way to acknowledge that there are indeed differences, so they are not in disagreement with this point.
Rather, The argument is that it's difficult to make a clear connection between these low-level 'nature' difference and the much higher-level issues we're discussing. That seems like a decent argument considering 1) how much of our world is socially-constructed, and 2) how often the argument '<group x> is inferior at <thing y>' has been used to maintain the status-quo by the status-quo, and more importantly how often it has been proven wrong.
To be clear, personally I'm in the 'genetic differences matter more than we think, in general' camp, to an extent that I don't always feel comfortable talking about it in public. And I do think there's something of a bias in the social sciences towards blaming nurture over nature.
However, first of all I'm not sure if, in practice, this bias is a bad thing for society. But even if it is, arguing that male babies act different from female babies and that somehow this explains many of or societal issues strikes me as extremely spurious and downright disingenuous when such an argument is used against people who already openly acknowledge that there is clearly a genetic element to the whole story.
Furthermore, while things might be different in SV, in my neck of the woods I'm pretty firmly in the SJW- or feminist 'circles' and I rarely meet anyone who truly believes that there are no genetic differences. It strikes me as odd that so many arguments primarily argue against the view that it's '100% nurture/cultural', when as far as I can tell very few people actually defend this point of view. It reeks of strawmanning.
(not that these people don't exist, I'm just saying they're a vocal, extreme minority in my day to day experience)
As to that one link, one study is not conclusive – animal studies are notoriously prone to unintended experimenter influences – and that's especially suspect when e.g. it claims innate color preferences for the pink/blue divide which has been biologically predetermined for about a century.
Again, I'm not saying there aren't differences or that they can't be significant, only that the research thus far doesn't support the sweeping claims being made.
I'll let you decide (Occam's razor is helpful) whether that is more likely the product of biology or "social expectations in early childhood" (within 2 days? in monkeys?).