As long as you copy from the same project that should never happen at all, which is probably the main use case. And if you copy from a different project then you can have a new paste command that would create new layers for the copied items.
After pasting there may be more layers than necessary but together with the possibility to combine layers that are the same this would allow to handle new items with all the layers they need and still be able to cleanup if necessary.

Would that be doable?