It's hard to control for social conditioning. I don't need to be able to tell you what the alternative is to be able to tell you that there are many confounding factors.
Knowing what does not explain something, doesn't tell you what does explain it.
They did try to account for social conditioning: parents' education and jobs, local labor markets, school performance, the whole bit. The gap still didn't move much. If socialization were the main driver, you'd expect the most egalitarian countries to have the smallest gaps. They don't. In a lot of cases it's the opposite. Sweden, for example, shows bigger differences in occupational preferences than places like Pakistan.
So at that point you're not pointing to a specific confounder, you're basically saying "maybe there's something else." Sure, logically you can always say that. But if the evidence keeps stacking up in one direction and the only reply is "could be something," that's just refusing to update your view.
Congrats! You've made your position unfalsifiable.
When the data consistently shows gaps widening as social strictures loosen, and your response is to blame an invisible, unmeasurable "conditioning," you aren't doing science at all. But you are insulating your belief from any possible counter-evidence.
No I'm just clear that the current state of science makes it impossible to draw the conclusion that you are.
Note that this outcome goes both ways. We can neither confirm that biology is the main driver nor confirm that it isn't. Life is not as certain as you want it to be.
They're not contradictory in a vacuum. But in this sequence, they show you're backpedaling. You opened with a firm claim, and when confronted with actual data, you retreated to 'we can't know.' Pretending that perfect certainty is required here is just a dodge.
Knowing what does not explain something, doesn't tell you what does explain it.