Since I can't see how they are doing the layers, I'm only guessing. But, they could do something like this...
Skin Layer 1 (Lightest Skin Tone - Fair)
Skin Layer 2
Skin Layer 3
Skin Layer 4
Skin Layer 5 (Medium Skin Tone - Olive)
Skin Layer 6
Skin Layer 7
Skin Layer 8
Skin Layer 9 (Darkest Skin Tone - Black)
Granted, it doesn't have to be that extensive, could probably do it with just 5, but it's just an example. Each skin layer is a different shade of color tone. You could incorporate that into the DNA based system by assigning a skin tone to a character. The offspring between 2 characters (man and woman) would be the averaged number between the two. For example, you have a male with a skin tone of 5, and a female with a skin tone of 1, and their child would have a skin tone level of 3, which is averaged between the parents.
I would prefer that it not necessarily take the average, but allow the complete range between the two to be available to the offspring. Therefore, using your example, if the father is a 5 and the mother is a 1, any given child will be between 1 and 5. A child isn't necessarily going to look like a meld between its parents.