The way I see it, Karkats blood is a mutation from having a Highblood and a low blood mixing, the mutation takes place because the low bloods genetic material is much thicker than highbloods, so they contradict and create the mutation that has changed over time to create Karkat.
Karkat's-and all mutant bloods- could have gotten thinner genetic material, so when a low blood mixes with a mutation, another mutation takes place, either a mixture of two colors, or a whole different color entirely.