The mod will not work if any of the items being used in the recipe are the same thing but from another mod. In my particular case another mod also has copper nuggets, and while most copper nugget recipes will accept either copper nugget the recipes from Create Deco will only accept the nuggets from Create. Can this be changed so that the recipes accept "any:nugget_copper" or whatever for better mod compatibility?

I'd recommend Almost Unified. It automatically merges metals and ores and whatnot from various modpacks.

This same issue also causes problems with Create Crafts and Additions. Both this and C&A adds zinc plates made by flattening them. Since this mod uses internal tags very specific to this mod rather than forge tags (forge:plates and forge:plates/zinc), they are not seen as the same item so these mods can't be used together seamlessly.
I fixed the problem by using Almost Unified, as stated above, with some extra configs. But preferably this should be fixed by changing tags to use forge-tags where possible

Create Deco makes it's own tag system and doesn't use forge or fabrics: see there: #114. Maybe I'll start a pull request for that.

Pull request is out!!