Does the atmosphere itself track the ground? I'd expect the slow rotation to drive persistent winds, potentially keeping weather systems somewhat tidal-locked as well

True but you basically lose the benefits of being on a planet. The point at which you're just floating in atmosphere I would argue you might as well be in orbit for all the resupply complexities, but few of the benefits - I.e. an orbital structure without significant atmosphere around it means high Isp low thrust engines like ion drives are practical to come and go from it and a lot of the energy is free from solar.