"So they must have some positive effect on genetic fitness to even exist at all."

That's not true. There's a number of ways variants can exist without being fit. They can be regularly created by mutation, or they can increase due to genetic drift, especially in a bottleneck scenario. And there's even more ways that a phenotype can persist while being highly unfit - if it's a side-effect of a co-evolving pathogen, being one of them, as then the human natural selection is constantly fighting it but the pathogen easily evolves even faster.