In a reality where multiple universes exist and god-like beings evolved, these "simulations" could be full (or simulated) universes where the physical laws have been altered.
They don't have to be big to make a difference, such as Na "liking" F more than Cl. No "table salt" could mean a completely different type of life evolves, maybe no life evolves, it's entirely up to you as the storyteller.
You can even make time a variable, so that an entire universe is created from Big Bang and ends in the Big Crunch in the matter of minutes to the observer, but the time within the test universe took many trillions of millennia for things to happen.
The exa-humans (or whatever they are called) doing the experiments would think of the beings within their simulated universes as we would amoeba: interesting forms of life, but expendable when it's time to end the simulation/clean the petri dish.
Also, a computer made by the "experimenters" could be so powerful as to create a simulation so realistic as to render it so realistic as to make it seem real to those inside the simulation (think The Matrix). Beings that seem to be self-aware and able to make non-deterministic decisions could simply be bits and bytes, and not even realize it.
At this point, super-powers are just one variable in the cosmic equation that you, as the story teller, can create and set your own parameters for, without the necessity of realism outside your story.
This could even go so far as to one simulated being having a power like Deadpool, knowing that it's a simulation and then escaping the simulation.