I forgot that Doom outsmarted the Beyonder and stole his abilities. The Beyonder was basically omnipotent. Bearing that in mind Doom can and probably will defeat Superman. Doom doesn't need to resort to brute force, he has more than enough time and he's diabolical enough to outsmart Superman. Green kryptonite laced armour? Red Sun radiation emitter? If I can think of these things, Doom can and will make them within a week. Plus he has magical ability to which even uberpowerful precrisis Superman is vulnerable.