I was under the impression that the jersey system was meant to reduce color ambiguity, but that it was separate from color blind support. The best way to reduce color blind confusion is to add textures, not necessarily shifting colors. For color deficiencies, shifting certain colors helps, but it could be difficult to know how altered colors would appear to someone without perfect color fidelity.
I’m red-green color deficient, but the only civs I've ever had trouble distinguishing was Civ V Poland from barbarians, and Sparta from England in VI.
For my two cents, the New England color was true St George red (but it did look slightly orangey due to being used to the burgundy color I’m used to. Poland in VI has a slight pink-ish hue to it.