Here is what I do. Usually compounding, polishing and waxing don't produce much dirt just polish and paint residue. Mine are never black with dirt. I do have all my towels color coded. one's for compounding, polish and LSP's.
I keep my polish, compounding and LSP rags apart from the grime one's. Grime goes in one load cleaner one's go in another load.
I never had to deal with cross contamination issues using my routine.
Before your towels hit the washer. Run a extra large load of cold water and 3 cups of vinegar no towels. Fill the liquid fabric softener to the top with vinegar as well.
When that is done wash the "clean" towels first warm water, MF wash. Add ball park two teaspoons of vinegar to the fabric softener cup for each towel. Only fill the washer up with water until it is a inch or two above the towels. This will force the towels to scrub each other rather then float around in too much water. When it's done. If they still smell like vinegar do a rinse cycle of water only. Just fill water like above.
Repeat for dirty towels.
When I'm working I have three buckets with water in them and a little APC. A gallon or two of water and a half a cup or a cup of APC. I use Purple Power since it's cheap. One for dirty towels,one for pads, one for the cleaner towels. I keep them in there until I'm ready to wash. This will help keep any chems, oils and debris from setting into the towels and pads. Wring everything out and do your washing. You will be surprised the amount of polishing oils, sealant and wax residue that float around in the water while they are soaking. The point is to keep anything from setting into the fibers. Wanna have a a really clean junk towel do it this way and you will be surprised.
I have worked on this for a long time and finally got to a point where I don't need to run the washer for a few towels. Doing it this way keeps all my towels spotless and free of debris.