I transform meshes into world space and use insertObject() with the identity matrix. That means that often the same source mesh is inserted multiple times. However my understanding is that Umbra does not instance internally so I'm not losing anything by doing it this way. Can you confirm that this is the case?
Umbra only uses instancing when serializing the Scene object to make the .scene dumps smaller to make them more convenient for storage and sharing. The Tome does not benefit from the instancing so your approach is 100% correct.