The separation of layers within objects comes into its own when loading the item into layout really.
It works in this manner:
Items in the same layer of the same object are treated in layout as a single entity, so all translation/deformation tools will work on everything within that object layer.
Items in different layers of the same object are treated as separate entites within layout. However, all object properties defined within modeller (such as your layer heirarchy) are preserved and loaded in with the object.
Items in separate objects are entirely separate and have no inter-relationship within layout.
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