Something to consider here is that the story's lore isn't written beforehand and then pieces moved to suit the story; pieces are added in to facilitate the story the writer(s) want to tell.
Zodiark's darkness wasn't a threat in and of itself - the threat was what his controller(s) wanted to do with him. The implication is that yes, the Ancients would have eventually ended up wiping the planet barren of life in their attempt to restore Amaurot, or otherwise left it in societal stasis until their inevitable end. The Plenty from the Dead Ends are very much meant to show what Amaurotine civilization could have become if they had actually succeeded.
Zodiark and Hydaelyn are unique among primals in that they were made with real creation magicks - the primal summoning rites are bastardized (for want of a better term) versions of this and come with some caveats, the excessive aether drain and tempering chief among them. Zodiark still needed to consume vast quantities of aether to do his mojo, but such a thing as terraforming is no mean feat even for beings as powerful as the Ancients.