Yes, the energy of the system still has to be preserved.
But we're not talking about moving the Mageddon, we're talking about moving some of its gears, and I don't recall any mention of a correlation between the two.
The only explanation we ever get is far too nondescript to reach any meaningful conclusions of what's actually being done.
Friction plays a huge role too. Each gear exerts a fictional force on another. For example, moving 10^20 gears has an insane amount of frictional force to overcome. Then you have just moving their masses as well. So even if there wasnt any load then it is still an insane feat.
It appears that Superman wasn't moving a large distance. So he didn't receive a large mechanical advantage.