I think it's just a genetic trait since they can breed for it. I did find this snipette:
"It is told, that Native Americans referred to the dogs with mixed eyes as "spirit dogs", and considered them a gift and of great honor."
Their stare is sort of disconcerting. It's intense, like any herding breed, but the two different eye colors really puts the whammy on you, lol. I can see why the tribes in the area would refer to them as "spirit dogs."