It really seems fixed to me. I don't really use SimPE (I'm making my first tentative steps with it), so I haven't checked to be sure. As for skintones, do they even keep recessive genes? I heard that it could be any skintone in the range between the skintones of the parents.

I love Pixel's alien eyes too! I use her defaults in my game. I never considered giving the contacts to Johnny (though I have been thinking that Jill might do it at some point to be more alien-like). His normal sim eyes may not make sense gentically, but neither do the rest of his features, so I like keeping him as he is.