Think of it like comparing bats and birds. Both fly and have some overall similar characteristics, but both are clearly anatomically different, and evolved from totally different lineages.
Same with snakes and legless lizards. Their skulls and much of their physiology is quite different. They are more related to each other than bats and birds, because they’re both reptiles, but really they have a lot of differences.
One interesting tid bit is that the skin/body of snakes can stretch, to swallow large prey. Most reptiles, and lizards specifically, can not stretch their skin, and so legless lizards only eat small prey, like bugs. They cannot stretch their body to swallow something like a mouse, and their mouth cannot unhinge itself like a snake to fit something that big into their mouth either.
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