The differences in DNA sequence are built into the genome of the Kind.
You already know that this cannot be true; since living humans (not to mention other species) encompass more genetic diversity than can be contained in the maximum 4 alleles Adam & Eve could have possessed for each gene (a diversity you opted to reduce to only two alleles, for reasons I didn't grasp).
I understand that what you're trying to do is find a way to fit the evidence to match the biblical account you accept as unimpeachable - but you should not be ignoring what you've learnt in the process.
Re: Simple Example -- any new mutation is outside the kind?
He was also a staunch anti-evolutionist. Back in college (late 1980's verging on 1990) I personally read an English translation of his Théorie de la terre (Theory of the Earth). From his Egyptian Campaign (whose other contribution was to use the Sphinx' nose as artillery practice, thank you very much, Nappy!) Napoleon had brought back many Egyptian artifacts, including a large number of mummies of both humans and animals. Those mummies dated back to thousands of years BCE; according to Wikipedia, the oldest animal mummies date back between 5500–4000 BCE, well before the Flood (https://en.wikipedia.org/...d_non-human_animal_mummification).
The problem for him was that he was still a young-earther. So he looked at the mummies from thousands of years ago, very shortly after creation by his reckoning, and he looked at the same modern animals and he saw virtually no change at all. Therefore he deemed evolution to be impossible.
Minor point, but I don't believe Cuvier was a young earther. He believed that humanity had only been around for a few thousand years, but he noted the enormous variety of extinct animals identified from fossils, and believed that there was a world before humans. The purpose of the Théorie de la terre, the book you mentioned, was to explain what was known at the time about "the series of events which preceded the birth of the human race", as Cuvier put it. While I can't find any claims about numbers of years, it clear that Cuvier thought the world had been around a long time before the few thousand years he allowed for human history.