The easiest way to explain this question is with a thought experiment:
Consider God, the ultimate of everything, who is wholly omnipotent (all-powerful) and omniscient (all-knowing). Let's just say, hypothetically, that he wanted X group of individuals to save a man from under a burning car (this is a totally random example I just happened to be reading about; I could have just as easily said He wanted Bob to score a free-throw in basketball 3 times in a row tomorrow, or Sally to knit a blue sweater on Sunday, November 4th, 2012).
But anyways, one way He could do this (get X group of people to save a man from a burning car) is: At the beginning of time, God could instantly plan out the future and set in motion a massive chain of events, from the creation of light and stars, the creation of Earth and the creatures, mankind, then civilization with all the conflicts and progress and glory that comes with it, such that one day, a few people would come from out of nowhere—complete strangers to each other—and save this man (also a stranger) from under a burning car. God need not intervene at all this whole time, He merely "ignited" the chain of events from day 1 and watched it unfold exactly as He planned. Let's call this Universe A.
He could also, being all-powerful, just freeze time for a bit and skip a few steps, creating the world and universe instantly, with all the civilizations and animals and things in place, putting all the strangers there together next to a car which is already on fire and the man trapped under it. Then press play, and presto, you have the exact same scenario, without billions of years of buildup. Let's refer to this as Universe B.
God is obviously capable of doing both. My question thus is whether there is an ontological difference (really any difference at all) between Universe A and Universe B. Personally, I don't think this kind of power is outside of God's capability; he should, after all, have no problem with creating identical universes which match up exactly once they reach "biker under the car" moment where He unfroze time in Universe B. At that moment, Universe A and Universe B are exactly the same, right? Or is there somethinge special about Universe A, with all it's buildup, that separates it intrinsically from Universe B? In other words, is it outside of God's ability to make them exactly equivalent?