I'm not sure who told you that. The dark yolk doesn't indicate a difference in protein from eggs with paler yolks. To the best of my knowledge, none of the amino acids contribute any color to the egg yolk.
Chickens don't assimilate carotenoids in their food so it ends up as yellow/orange coloring in the yolk. The more they consume, the darker the yolks.
Free ranging chickens in mild climates with access to tender green growth will have darker yolks due to the various carotene compounds. Marigold, pumpkin, sweet potatoes, kale, spinach are things that will make yolks dark. NOTHING about those foods will increase the protein in an egg. The reason store egg yolks are yellow is because they are fed feed with yellow corn as the main ingredient which provides the carotenoids lutein and zeaxanthin.
In some parts of the world (i.e. Africa) white corn is a primary ingredient. Their egg yolks are extremely pale. That doesn't mean there is less protein than eggs from free range flocks with access to the foodstuffs I mentioned with dark yolks.