The nakedness is due to the feather tract growth tracts being stopped about halfway through. Feathers in most birds start out in specific locations in the embryos and those then grow outwards to cover most of the bird. These are "stopped" about halfway through in birds with the naked neck gene.
The varying degrees of nakedness you are seeing probably is the visual difference between those pure and not pure for the naked neck gene.. the feather tract growth apparently is stopped a little sooner on pures than on those not pure for it.
I'll put up pictures of day old chicks showing the difference:
This chick is homozygous(pure) for the naked neck gene:
All of those are pure, except for the dark blue on left:
Same two blue chicks in above pic:
This one is good for showing the differences on the face: left has a full fuzzy face while the one on right(pure) also has naked area between eye and beak(same as chick in top picture).. also note bowtie size difference. Pures have a small one with the lower front being very visible while not pure ones have a larger bowtie which often covers the whole lower front of neck.
While they grow.. even the not pures can look rather naked before the feathers come in then the visual difference is obvious again.
Another tricky part to breeding them is the comb type.. all above chicks are single combed(the blues are full siblings btw).. Pea comb gene also has a side effect of reducing the overall number of feathers on the bird and this becomes readily visible on a pea combed naked necked bird NOT pure for it- those can look as naked as the pure single combed birds. I haven't seen anything written about rose comb having an effect on feather number, however I have noticed rose combed naked necks often have slightly smaller bowtie size, usually in between single and pea comb in size.
If you got the eggs from someone, it's extremely common for people to miss the clue of bow tie size differences and so pair up two not-pures(about half of hatchery stock are not pure btw).. chick ratio from this is 1 not-naked, 2 naked necked but not pure and one pure naked neck.
With single combed birds, it's extremely easy to create a line pure breeding for the naked neck gene. Simply keep the ones with small/tiny bowties and you're set.
Sometimes there will be the claim that only the totally bare necked, as in no bowties at all, are the ones pure for the naked neck gene however this isn't true. I don't know what causes totally bare necked birds, possibly an extra gene or ?? that acts as a modifier?
....I've also noticed the varying degrees of nakedness amongst these newly hatched fuzzies.
