That's a really intriguing article. I found it interesting that they showed a Boxer getting swabbed because Boxers that are all white tend to have other problems (deafness comes to mind), so the genes that cause coat color definitely seem to be impacted by other areas of the dog.
Though you wouldn't guess it looking at an Irish setter, all coat colors are modifications of black and yellow. "A Dalmatian looks white with black spots but based on its genetics it's black. Dogs that are chocolate—like one of my dogs, a chocolate poodle—are also a modification of black," said Barsh. However, his other dog, an apricot poodle, is genetically yellow, as are Irish setters.