Thanks for bringing this up, @McComb! I also feel it would be really valuable to have some degree of administrative control over the gender classification question.
A challenge is that the Man/Woman identity has an operational function (e.g. preventing someone who identifies as a Man from enrolling in a Women's league).
However, one way to work around/with this is that if a registrant selected a third gender option (e.g. "Another", "Other", or "Prefer not to disclose") then they could be allowed to participate in leagues that are set up as Open (no gender restrictions) in IMLeagues, but not Men's/Women's/Co-Rec. Given that it seems many schools are going the route of Open leagues any way, this minor change could go a long way toward supporting students who identify outside the gender binary.