Interesting! I guess this would potentially imply that Godzilla isn't actually a reptile (or even a tetrapod for that matter) if his ancestors originated from the sea first and he's a "sea animal becoming a land animal" and not a "land animal becoming a sea animal" like real tetrapods. After all, reptiles are ancestrally land dwelling in our world and no land-dwelling tetrapod, as far as we currently know, has ever became aquatic and then switched right back to living on land after already adapting for water. If, in fact, Godzilla's species is basal to where his evolutionary lineage to start living on land and he's not a land creature adapting to an oceanic life, then he'd only be very, very distantly related to reptiles and all of his similarities with them would be pure convergence. Either that or, unlike in our world where all land dwelling vertebrates share a common ancestor, all land dwelling vertebrates in the Tohoverse are (sorta) unrelated and independently evolved to live on land from different types of fish.
Sorta like this, but to a more extreme degree:
Tetrapod evolution in real life:
Whale evolution from land-dwellers to sea-dwellers: