Remember in this case the simulation is not running a model of physical reality - it’s only running a neural net that is fed into your senses.
In that case there are no ‘atoms’ it’s just a concept fed into your mind. Just like in dream it’s hard to question reality, you just go along with it.
It's equally important to understand and study the rules of this waking dream you are having while reading, not because there are actually atoms out there but because it behaves like there are. You can do physics without metaphysics, altough the two usually get entangled somewhat.
Conventional physics giving birth to our universe is currently the model with the fewest assumptions.
What would have to take place to give rise to a universe the size of a data center, running an AI model of a human? It feels like we have to bake in assumptions of stable physics, a rise of a stable system for that data center, and some path towards creating it and modelling a human.
That said, if we believe we're capable of running billions of believable simulations, then we're more likely to be in such a simulation than ground reality. But a datacenter pocket dimension bakes in a lot of assumptions that make it less likely than our own universe.