Honestly I’m not to sure on how it works as I’ve just started recently playing with the overrides. So you may have to ask in another section of the forums or hit up @hunterk and see if he knows.
I don’t think you have to make individual presets for systems though, most likely you just set everything up how you want it for the system and then make a content directory override. As the override is well, an override (so it overrides w/e differences there are between the main cfg and the override config, at least this is my assumption.) If someone actually understands this stuff and I’m wrong correct me please.