The bigger difference imo is the brain development due to hormones in the womb. Old TLC program had a whole section on this suggesting it's why STEM fields are generally male dominated. Turns out hormones that determine biological gender also very much effect the development of the brain, and the male chemicals tend to develop the spatial reasoning part of the brain faster/more thoroughly than those who get don't get the male chemicals and stay female. This average higher spatial reasoning capacity creates an advantage in tasks or objectives where complex visualizations are necessary, like visualizing chess moves in your head.
It's not some massive, overwhelming difference, but it's enough to tilt the table. Play out that average enough and you have 42 women out of 2500 chess grandmasters