Nice story, each paragraph is pretty densely packed with layers of meaning and wisdom about our own existence and nature of reality.
Although this is pure fiction and speculation, thought experiments like these (existence of free will, laplace's demon), rely on determinism.
Even if we assume the universe to be completely deterministic, we need to "know" the initial seed state (usually called big bang).
That initial seed can and will create vastly different universes (similar to how changing a single pixel in Conway's Game of Life completely changes the emergent behaviour and properties of the patterns, often just destroys the apparent stability in the system).
So, even with the an all powerful quantum computer, the initial state will give vastly different universes (all of them consistent within but not with each other).
We can think about "what" the initial state is ? Is that initial state self contained ? or was it under effect of something else ? Will the computer "generate" the initial state, or the programmer (aka god) has to explicitly hard code it carefully to create an apparent stable universe ?
If time as we know it, started with the big bang, the no notion of something existing "before" the big bang, doesn't make sense. If time existed before the big bang, then big bang is not the actual initial state (it is an initial state for us, as we cannot know outside the big bang, i.e. the universe).
Therefore, all simulations considering that to be the initial state will be incomplete and incorrect. Maybe we simulate what we can observe with our senses (directly or indirectly), and that will give us a "valid" simulation. For us, that is a perfectly valid simulation, but for the "things" that were before the big bang (if you assume that time was present before big bang), our simulation will have an extremely low entropy.