I mean, whatever propensity to mathematical-logical thinking, or being interested in working with things not people, we attach to software engineering, aren't these qualities useful even more when doing math and physics?

Lots people from math and physics have jumped over and become decent, some even great, software engineers. Not many software engineers have successfully switched over to math or physics.

So if gender is not so much an issue for a successful career in, I don't know, algebraic topology (math) or quantum field theory (physics), it surely should be less of an issue in software engineering ...when talking about whatever effects there may or may be at a biological level. So if it's not such a big issue in academia, the problems in software engineering must be more about what kind of workplace culture has grown around in software engineering, not the proposed underlying human biology.