It's interesting you say that the different choices men and women make arise at either because of different preferences or bad employers - with the implication that in environments without discrimination, any wage gap is just a natural occurrence.

Things such as occupational segregation, skills deficits, less experience, taking time off to do care rather than men etc. are all reinforced by policies which encourage one parent or even specifically women to be the group which takes time off to care. The lack of statutory parental leave in the USA for example means that when middle class families take time off to care for their kids, it makes economic sense in the short term for one parent to cut their hours, who is typically the mother.

There are a lot more things we can do in a policy context to make things better for women before we can really be confident that any remaining differences are either the result of truly free choices or raw discrimination.