I think we at least need a way to add an ID to the main Layered material so you can get a mask for the complete shader. Or if this isn't possible then at least remove the button - I think that if a button is there then it should work.
I believe in vray that each sub-layer can also contain an ID. The best option would be to have the ability for separate IDs for each sub material and also one the main layered material.
Then the question would be what which would override the other if the main layered material and one of the sub-materials has the same ID assigned. I can see arguments for both but I think the main layered material should override the sub-material if they share the same ID.

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