Classwork isn't some static thing; historically, boys had higher GPAs than women, and I suspect you can find some subfields of study today where boys consistently outperform women as far GPA goes. The choice of what subject matter goes into the curriculum that a GPA represents and how's it's taught and evaluated is a political choice. You could very easily make GPA equitable by removing one class that girls over perform in and replacing it with a class that boys over perform in.
The truly awkward question is that GPA is important because colleges give grades too, but maybe the classwork grading and tests are bad and not conducive not education overall.
I'd be interested in seeing if there's a gender effect on how predictive SAT scores are on college completion rate. A quick survey indicates that this isn't an area education researchers have thought is a good use of their time.
