Region printing with different setups is a breeze when your regions are easily defined by Z axis only.
Slice3R has an interesting feature that allows you to define a region by an intersecting volume on top of this.
This feature is really convenient when you have a part which need reinforcement in particular regions, leaving other less filled.
Only tricky thing is to import and position parts against each other, which can be done easily in most CAD software, by example when saving assembly as STL.
Why not define body intersection as a region?