If I'm not mistaken, the episode doesn't outright state that the Voth evolved into sentient beings and developed space faring technology while they were still living on Earth. That was more of a supposition.
It's more likely that some advanced alien race, like the Preservers, saw the incoming cataclysm, or its immediate aftermath, and decided to relocate the ancestors of the Voth due to their potential.
My biggest pet peeve is that they claimed the Voth descended from Hadrosaurs, which were basically the cows of the Jurassic. They should have been descendants of a species like the Troodon, which was one of the smartest dinosaurs, apparently.