I like the Tarnished Archeology theory that there was a war between Leyndell and Mt. Gelmir and that Messmer fought on the side of Mt. Gelmir/Serpent god and as such was ostracised from Erdtree side. His throne is missing from the Morgott arena and he has snakes about him as well.

But I don't see any other lore slingers validating this theory so I am unsure. It would be cool nonetheless .