Ark Sky - the genetics your sim babies inherit from their parents fall in a sort of table like Gregor Mendel might have made
Male parent dominant || Male parent recessive
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Female parent dominant || Female parent recessive
The odds of the dominant for one parent being the skin tone you see is dependent on the "darkness" of the skin tone
Let's assume the Maxis skin tones are give the following values:
1 - light
2 - tan
3 - medium
4 - dark
5 - custom skin tones
(it's a bit more complicated than this, but these numbers will work for this illustration)
If you Sims are made in Body Shop or Create-A-Family - they have as their recessive the number for whatever the Maxis skin tone that was used for the base of the custom skin tone. So even if you have a sime with a custom skin tone, he or she will always have as the recessive gene the Maxis default.
So let's assume you male parent sim has a light custom skin tone, and your female parent sim has a different light skin tone:
5 (a) || 1
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5 (b) || 1
The possible results of this pairing are:
Gene pairs
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5 (a) + 5 (b)
5 (a) + 1
5 (b) + 1
1 + 1
as you can see there is a 1 + 1 pair-up of genes -- so the baby has a 25% chance of getting the Maxis light skin tone (or your default replacement)
in the case of the 5 (a) + 5 (b) pair, it's a 50/50 chance either will be inherited.
If one of the parents has the Maxis light skin tone (even when a default replacement) the chance of a light skin tone being used increases to 50%
there is never a 100% chance that a baby born in-game will inherit all custom content - only the promise that it will be treated with a normal genetic preference as a dominant.