I've got some request about baking ID map. Please add options to bind individual color ID to material. There was situation when after baking maps in Toolbag and painting lowpoly in Substance I needed to back and split some parts of the model, modifying and assign new materials. After rebake new models HP to LP in Toolbag, ID map has new random color set. So I needed to reassign it again in SubstanceP.
(Or I missed something.)