What I found strange about the reaction to this paper was that it could equally well have been read as “Look, people with female mentors seem to have poorer outcomes, this means we still have work to do to increase the effectiveness of female mentors”. Perhaps female mentors try to fight equally hard as male ones for the resources that their grad students and postdocs need, but are held back in that by the patriarchy. I don’t see what’s especially controversial about “We haven’t fixed sexism yet”. Indeed, the people I see most often patting themselves on the back for having fixed sexism are senior faculty, usually male, congratulating themselves on some bureaucratic initiative involving a lot of people saying “sexism is bad, m’kay”.
For what it’s worth I thought the article wasn’t very good — some of the assumptions and measures they used seemed very simplified — but it does look poor when research by two women out of three authors gets called misogynist.