You do realize that there is no Big Tree that represent Yggdrasil in tbe game, right? The tree in the picture is just the 4th gym. Depth can refer to the deepness of the earth, not necessarily the sea. And a snake is very commonly associate with the earth. Beside, it's Niddhog that's supposedto be destruction. But in the game, Yveltal is.
And there was no biblical apocalypse in GIII, but that didn't change them being Behemoth and Leviathan.