What seems to me to be going on with mojave and lesser is that they are _different_ mutant versions of the _same_ gene (i.e. alleles). The differences and similarities are both important.

Usually we know of only two versions of a gene. For example the mutant striped version and the normal for striped version of the same gene at what we might call the striped locus. I think the human ABO blood types are examples of a gene that has more than two versions. It's looking like for some reason the white snake complex gene (probably need a better name for that, especially since some of the supers aren't so white, like the homozygous phantom) has a bunch of different versions.

Evidence to support lesser and mojave being mutations of the same gene includes MKR reportedly only producing lessers and mojave from their cross line leucistics bred to normals. If they where two different genes like the pastel and cinnamon that combine to make pewter then some normals and leucistics would also be expected.

Evidence to support the mutations themselves being different even though of the same gene include the two lines looking distinct still after lots of outbreeding to a variety of normals. If the initial differences where just family resemblance in the founders the lines would have been lost by now through breeding to so many normals and probably in some cases the same normals bred to both lesser and mojavies. Even if it turns out that it might not always be possible to tell the darkest lesser from the lightest mojave the lines them self are still distinct with the average lesser looking different than the average mojave in spite of some possible overlap.