One thing to keep in mind is that if your setting lacks in-depth knowledge of biology, having your explanation for gender or sex specific magic be based on in-depth biological knowledge creates a tonal conflict. Or, if that is not clear enough: don't use chromosomes or genes as an explanation if the characters in the setting can't be expected to know about that!

Instead: if magic in your setting is primarily theurgic, accept and embrace the fact that magic is gate-kept by one or more supernatural beings. In your case: Baphomet or avatar of it arbitrarily decides who counts or doesn't count as a woman. If you want to emphasize mysticism, you don't need to tell the criteria to the players. Leave them up to their trial-and-error. This also shifts the burden of introducing transsexualism (etc.) to the game on the players and minimizes chances of it becoming a focus unless the players really want it to.

If you do wish to reveal the criteria, put it in terms which would be comprehensible to both players and their characters. For example: if womanhood in Baphomet's eyes is based on ability to menstruate, that's a clear cut on who makes it and who doesn't. If the players or their characters find this offensive, they are free to go the usual "God(s) is (are) EVIL!" route.