Hello there.
The additive traits from this plugin currently all stack together when creating an item, with no plugin parameter option to change that. An edit, or addon to the plugin that makes it so that only traits that exist on more than one of the ingredients is passed on to the crafted item shouldn't be too hard to create, as the method used to add additive traits together on the result item is actually very straight forward, and should be relatively easy to build onto.
The only issue I can foresee with your idea, is that the crafting system only currently supports one 'wildcard' item per recipe. In Skyrim, a potion recipe was simply created by combining 2-4 ingredients, and any traits those ingredients shared between eachother ended up on the 'potion' (or poison). As this system currently only supports making recipes that have 1 random player provided ingredient in them, you'd need to script yourself different kinds of potion recipes that used specific ingredients and a wildcard ingredient.
To the player it'll look the same, but it's a bit more work on your part.
At any rate, if I get the chance in the next couple of days, I can see what I can do about taking care of that request.
-Ramza