You can design the algorithm in such a way that your priors are mistaken, or bias creeps in (though theoretically that can be self-corrected). But assuming that's not the case, and the algorithm correctly matches up mostly women v. women and men v. men in a skill parity optimization, you have a fair result for the purpose of a tournemant; i.e. skill-based match-ups.
If at that point you have an issue with the match ups for reasons of gender or ethnic parity, I would argue that you should seek to correct the upstream issues, not the algorithm. In other words, try to get more women playing chess - make the sport appeal to them more, make it more inclusive, etc. Rebalancing an algorithm is, in my view, a handicap, whether it's applied to gender disparity or any other disparity. I feel it does a disservice to both parties and doesn't really solve the root issue.