The custody gap is largely caused by different desires about custody. This is still an issue, but it is the same issue as the wage gap due to different career choices. When men and women fight for custody equally, they tend to get joint custody.
I agree that there is an interesting and potentially informative symmetry between the custody gap and the wage gap. They both describe situations that different groups find deeply unfair, but can be ascribed in large part to "different choices". It might be fruitful to take a more holistic view to understand why the "individual choice" explanation is so unsatisfying to many.