>snakes aren't lizards!
Both are Squamata, Pokemon does a lot of this, the reason Pikipek / Trumbeak evolves into Toucannon wasn't because of some random reasoning at Game Freak, but because both woodpeckers and toucans are Piciformes.
>b-but Charmander has limbs, it can't be the snake
So does the Snivy line, ancient basal snakes had limbs, and some modern lizards are limbless. It's clearly the same case of Fennekin, a fox (Canis member) is the Dog rep, Charmander the lizard (Squamata) is serpentine / snake rep.
>b-but Charizard isn't a snake, but a dragon (mythological reptile, can't be proper classified)
Typhlosion isn't a rat either, you only need a single stage to fill the requirement.