I know you’ve discussed that it is only for built-in materials, but I think it would be really useful if maybe after you select a material in the menu, you have the option to select one of the custom sub-materials from the drop down under said selected material. Of course you could just not select a custom material to begin with which would let it function as usual. This would allow users to swap custom materials easily as well. For example, you could swap a cobblestone for a custom corroded metal material. Or replace a custom with a custom of another type. That sort of thing.
While this plugin is useful, this functionality would really step up its use. You talked about pairing it with another plugin to do this, but in all honesty it would just work smoother, faster, and easier if it was cohesive.