I think you've hit the nail on the head. In D&D women and men are physically and socially equivalent in the rules, but for some reason some gamers like to keep playing up the realworld inequalities, regardless of how utterly illogical it is in the context of the game mechanics.
(In all fairness, though, surely someone somewhere has played the Amazon setting? Though of course that usually just swaps extant M/F disparities in the realworld; that is, it just slaps boobs on real world male stereotypes, and makes men effeminate.)
That said, playing the roles of women in the campaign Hunter99 has outlined, with the understood goal of bringing down that world's order through a combination of physical prowess, subversion, altruism, individualism, liberty, and all the other things these Orders apparently revile... now that could be an interesting game.
Assuming, of course, the subjugation, violation and rapey shinola is played way, way, way down by the GM.
I think both of these groups make for good bad guys and I can see a fun campaign built around trying to bring them down.
Some how though I have the feeling that the Knights of the Virgin are really supposed to be the bad guys and the Knights of the Scarlet Woman are his ideal. I think he is only giving lip service to them being evil.
I have Amazons in my setting and they don't subjugate men like this. They have a pact with a group of male Artemis worshipers. Once a year they have a feast and orgy for the purpose of procreation. Male babies are given to the men to raise and females become Amazons.