I like the op's suggestion although at my level it isn't a large issue i can still see the writting on the wall for the problem. To make this even simpler on the coding side just introduce new transmute recipies requiring transmute (kind of duh but hey keep the tradeskills intertwined) that make a specific type of rare from 2 of the existing types of rares for that tier. Meaning you don't have to change tons of recipes to require a "universal" rare, the recipies stay the same it's just the transmute recipies that are a bit more complicated or just more of them to keep it simple.
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