My first barn separated mares and geldings, except for one gelding who didn't get along with other geldings but did just fine with mares. It didn't bother me and I never really questioned it. My current barn's paddocks are based more on personality or owner than gender. And usually the "by owner" grouping is because those horses are attached, if not slightly herdbound, to each other.
Abby lives outside with her gelding underling, a mini mare, and her colt. I haven't watched for an entire day to figure it out, but the mini mare just might be above Abby (a 15.2hh, 1200lb horse, mind) in rank. Abby will sometimes graze right next to the gelding and other times she'll tear after him just to kick him a good one, then walk away. This summer when I worked at a summer camp, there is no way I could have kept Abby with the lead mare of the camp herd, had they been separated by gender (they're separated by camp horses and wrangler-owned horses). Had I done so, I would have had two heavily injured horses, if not worse.
I like the separation based on personality more, but I have also never had geldings "claim" mares or anything like that.