Unfortunately, many breed characteristic decisions were chiseled in stone in a standard before we understood the actual breed genetics. Nankins are a prime example. The original European standards for a yellow bird (the name "Nankin" derives from "Nankeen" which is a yellow cloth) were forsaken by APA and ABA for a "mahogany" rooster and a somewhat lighter hen. If you breed any set of Nankins long enough, they will produce lots of lighter roosters and hens,which is closer to the European standards and probably closer to the original breed. Some people cross Nankins with other breeds to get the darker mahogany rooster, more like an Old English Red Ginger than like a yellow rooster. With that cross you do get the darker roosters, but you also get the penciled, darker hens. Ironically, the yellow Nankins themselves will evolve (if you don't cull them) toward the penciling in the hens, which is evidently a normal "wild" trait that allows a hen, and her chicks under her, to hide from predators more effectively.
I understand that there are similar issues in the Ameraucana coloring lines, due to the standards being "voted on" instead of researched.