Well, yes and no. If your slice at 0.1mm with Hob3l, then slic3r can still decide that it uses 0.2mm or 0.3mm or 0.4mm slices -- it would just skip a few slices from Hob3l. I don't think there is a problem with that. It will get weird if you use Hob3l with 0.2mm slices and then slic3r with 0.35mm slices -- this will cause Moire effects. It is not wrong, but may look interesting...

Unless you have 0.1mm detail, in which case it will just disappear completely.

I think the eventual idea here is to have your slicer support .scad files as well as .stl files.

Yes, but it looks like it would still be impossible for the slicer to slice different height layers with this.