The answer to this question is the presence or absence of four limbs, on its own, could be misleading when considering the evolutionary relationships of rattlesnakes.
This happens when we consider the phylogenetic relationships between different groups of organisms using just one trait or a gene can give misleading results. In this situation, the absence of limbs is a new characteristic (snakes used to have four limbs like all the other vertebrates, and phytons and boa snakes still have some skeletal elements of the limbs in their bodies) so if we used the absence of limbs as a defining trait, that would mean that the rattlesnakes are more related to lamprey which are also limbless, than to other reptiles that have limbs, which is incorrect.