There can be a bunch of different alleles at a single locus that code for similar but different things. For instance, the Butter/Lesser etc complex you mentioned. Those genes (I believe) are allelic. They are similarly coding proteins at or near the same locus on the same chromosome. This doesn't mean the animal that receives one copy or the other are the same morph, it just means it received one of the many alleles that alter that particular trait. So a Butter/Lesser Super would produce all young that are either Lessers or Butters and (theoretically) you would be able to visually sort out which ones received which allele.

Does that answer your question?
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Lincoln, NE
0.1 Pastel, 1.0 Pastel het Pied, 0.1 Pied, 0.1 Cinn, 1.0 Black Pewter, 1.0 Woma (hidden gene?), 0.1 Yellowbelly
2.0 Normals, 1.0 Thayeri, 0.1 Thayeri X Alterna, 0.1 crazy cat, 1.0 husband

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