I really hope that KS stays predictable, so not to much 'auto changing' without warning. So if some repairing will be done with KS, I would opt for a clear distinction to have insight / do repairs, so there will be a distinction between the 'absolute KS' and the 'fuzzy stl KS'.
Regarding the void meshes: that option seems to get an own life, maybe similar to repair-like options but as modeler as well.
For me, the way KS now is working with the priority of submeshes and the void possibility is absolutely clear, but that is the option 1 you describe: as it is now? Or do I misunderstand that?
OTOH, right clicking on the model and having access to all that features on the Extruder mapping Window is (to me) clear enough, but would maybe benefit from a more extended window with options as 'invert normals of a mesh' void, and maybe the switch how to generate a support structure for that mesh.
Maybe others have some ideas about this as well. Penskeguy? ;-)
Bart