I just ran into this with a referenced rig that has script nodes kicking off script jobs when the file loads. This is great when there's only one reference. But it becomes a hassle when you reference in the same rig multiple times. I had to scan current script jobs to eliminate nodes/namespaces that have already been accounted for.
If script jobs can work in their native namespace by default, no energy would be required to even think about this. If it works in the original rig file, it's guaranteed to work in a referenced scenario...no matter how many times the same rig is referenced.