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As I understand it, if the skins are geneticized they're on a numeric scale. If the alien skin is also geneticized, then it's on the scale, and anything that comes between the alien skin and the parent's skin on that scale is possible in the baby. The weirdness comes in when you have skins that have been geneticized in odd ways (like bright color skins in which blue is 1.1, green is 2.1, and yellow is 3.4, so that breeding S1 and S4 has as good a chance of popping out a blue, green, or yellow-skinned baby as a maxis-skinned one) and when you mix skin sets that aren't scaled the same way, so that lighter Set 1 skins pop up when two darker Set 2 skins are bred.
Normally, alien skins aren't geneticized, which is why they tend to trump other skintones in alien births - non-geneticized skins are dominant. In that case, if the parent has a non-geneticized skin, it is also dominant, and it's a coin flip which you get. So if your default skins were non-geneticized, about half your alien babies wouldn't be green.
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