Spoke with dev about this. The combination of plugin and direct import definitely won't work.
We are making some significant improvements in KeyShot 7 where you can actually update multiple models in the scene. This is the fundamental problem here. You have 2 assemblies at the root level, so KeyShot doesn't know which on to update. At its core it is only meant to work on a single assembly.
To work around this issue for now you could try to create an assembly that contains both of the root assemblies as subassemblies. Then live linking or "update geometry" thought the importer will work without problem.
Let us know how this works for you.