Midgardsrmr probably couldn't match Omega, hence why it fled. Omega surmised that Midgardsrmr was inferior, though they didn't fight to the death. I think it's implied that Middy wasn't capable of defeating Omega.

Moreover, I think this whole origin story throws a lot of wrenches into the creation myth of the universe. As it stands, the cosmos was just a blob of aether until Hydy and Zodiark diffused from it to form the planet of Hydalyn and the moon of Zodiark. But it was sort of implied that everything beyond these 2 celestial bodies is pointless/meaningless and it's a geo-centric universe. With there existing other planets with their own alien life, it calls into question how important Hydalyn/Zodiark/Ascians really are. Is their conflict only important to THIS planet and other planets don't give a shit? What about those 13 parallel dimensions (shards). Do other planets get shards too if their sovereign gods splits into dark/light?