The magnitude of the bias reported isn't alarmingly high so some of the things you suggest and others might be reasonable to consider as origins of the difference.
However, the change of the acceptance rate histogram from uni-modal to bi-modal when the gender is known for a woman seems to be much stronger evidence of gender bias.
The bottom axis of the histogram is rate of code rejections for an individual, and the left axis is the number of individuals with that rejection rate. When gender is not known both men and women have dominantly high acceptance rates tailing off towards low accpetance rates. However when gender is know a sharp second peak at the 90% rejection rate shows up on the women's histogram but not the men.
Thus I think what this study shows is that for the most part women work on code in ways that produces code more likely to be accepted. The fact that it tends to be longer and not something on the bug list may make their submissions different (more substantial infrastructure not defect fixes might be one interpretation). So I'm not inclined to conclude much from that. But the bimodality seems to be evidence of a strong gender bias among a small number of open source projects.