Even if we consider that most of the universe is empty space. If one is all powerful you could make a more efficient universe. One infinite plane would be better.
More usable space. Better suited to life. At least better than mostly empty and unlivable space. This is assuming a godly creator who can do create the universe as anything.
Essentially if there was a godly creator they would be a Flat Earther if they were smarter. In the real world though Fat Earthers are wrong, and the globe disproves intelligent design.
Might also be limits? Consider making our world like designing a video game. Could literally anything be designed or would there be some universal limits?
Those benefits work in a universe that is hands off. A creator should have been able to come up with a better system than one that lead to most species becoming extinct.
I agree there are optimizations to be made, but every optimization could break something else. (eg allow FTL, now have to deal with time travel or something)