Perhaps, by sheer historical contingency, aspiring rationalists are recruited primarily from the atheist/libertarian/technophile cluster, which has a gender imbalance for its own reasons—having nothing to do with rationality or rationalists; and this is the entire explanation.

This seems immensely more likely than anything on that list. Libertarian ideology is tremendously dominated by white males - coincidentally, I bet the rationality community matches that demographic - both primarily male, and primarily caucasian - am I wrong? I'm not big into the rationalist community, so this is a theoretical prediction right here. Meanwhile, which of the listed justifications is equally likely to apply to both white females and non-white males?

Now, that's not to say the list of reasons has no impact. Just that the reason you dismissed, offhand, almost certainly dominates the spread, and the other reasons are comparatively trivial in terms of impact. If you want to solve the problem you'll need to accurately describe the problem.