Well, those are not exactly feats outside of the Doctor's reach. Written properly, he's the guy that solos the Big 7 JLA by turning the them into a park.
Plus, we don't actually have any clue as towards Doc Manhattan's powerlevel compared to, say, Superman's, because Doc Manhattan has never before fought or even met a superpowered being.
Omnipotent in a universe that doesn't superheroes or even magic in it is not the same as omnipotent in the DCU.