I wasn't thinking of them as levels, much more like wandering things you could tackle like the platforms/camps of enemies, just flying high enough that they won't usually bug you on the ground. Maybe if Magnesis was still a thing you could pull bits off them either to gain entry or to bring them...
Also it might be cool if unique enemies could be generated on the overworld map, similar to how the palette swap enemies start to appear as you get further along. They could have cool names and unique abilities. Maybe sometimes you'd get cool underground caverns where unique monsters from a set...