I have a similar problem with one of my patterns, it's for 50 states and I want to be able to use different states as tags for searches, but also like the variations option. So my compromise has been to use 4-6 different states as tags per listing and then have a few listings. But every single listing has all 50 states available as an option so the buyer doesn't have to go to another listing to find their state. does that make sense?
So if you want to do something similar, you could do 4-5 colors per listing and have maybe 5-6 listings to cover all the colors as tags. Then make sure you have all the color variations in every listing so people don't have to hop to another listing to get a color they want. This will save you listing fees as you will have a few less listings, and make it more convenient for your customers since they don't have to hop around to find the color they want.
Cheers!
Rachel