The material is the same, it's not like they're running on a different system. However they have a lot less genes and as such arent as complex as humans/mammals. Thus line breeding will have a lower likelihood of making a deadly/crippling/etc trait present itself.
It's talking about bacteria and how they developed differently between mammals and reptiles. That doesnt suggest that they have vastly different genetic design/composition. It simply means that reptile and mammal bacteria evolved down two different paths.
What we do have to support difference between them is that we line breed and it doesnt have much of a detrimental effect, pointing, potentially, to a narrower gene pool that doesnt have many genetic related diseases in it.