Instead of manually exploding the mesh parts, why not take advantage of Substance's ability to bake by name? You specify the high and low poly meshes, ensure that all the high mesh parts end with a suffix like "_high" and all the corresponding low mesh parts in with "_low", and let Substance bake them each individually from there?
Additionally, is there any reason to use Blender for normal map or AO map bakes at all? Why not bake all the maps in Substance using the high-low workflow above?
Hey Jesse, the exploding is needed for baking AO correctly (in either program) and doesn't have anything to do with baking normals in this case. The movable pieces need to be separated so that otherwise occluded areas (like underneath a movable switch) won't be turned black. It's also needed to be able to paint on the movable parts that would otherwise be hidden beneath other parts of the mesh.
I prefer Blender for baking normals and AO since I find it more flexible, but if it works for you to use Substance then there's no reason not to. Whichever suits your workflow best.
Hope that helps!