If we're part of a simulation, how likely is it that whatever it's running on is using the same sort of atoms we've discovered?
I think the answer is it's very unlikely. The closest resemblance I find plausible is that our atoms are simplified versions of the substrate atoms, and I wouldn't count on even that much.
I'm pretty sure that a simulation has to be smaller in some sense than the universe that's running it, which means that it has fewer things or simpler things (these might be equivalent because more simplicity means fewer sub-components in things) than the home universe.
You might do a meticulous job of simulating your matter in a simulation, but I suggest that you'd only bother in a small and/or specialized simulation, and even if you did, there's a reasonable chance that you don't have a full understanding of your own physics.
When I look at the range of human-created simulations (dreams, daydreams, fiction, games, art, scientific, political, and commercial simulations) and contemplate that we've probably only explored a small part of the possibilities for simulation, it seems vanishingly unlikely that we're in an ancestor simulation.
When I first came up with the question of the nature of our possible substrate, I didn't think there was a way to get a grip on it at all, but at least now I've got some clarity about the difficulties I think.
So onwards to practical questions. Is there any conceivable way of telling whether we're in a simulation and if so, learning something about its nature? Is it worth trying to get out of the Big Box?
Edited to add: I should think that being a simulation is an existential risk.
I use stronger language. The chance that we are in an ancestor simulation is in the neighborhood of epsilon.
All the arguments which imply that we might be living in a simulation would imply that the universe which is simulating us is also a simulation. I assume there's got to be a ground universe somewhere in the chain.
An extreme Singularity doesn't seem necessary to get a lot of simulations.
Whether we can be sure we've gotten out may be a different problem than whether we can get out.
I'm not saying you're wrong to think this is likely, but I don't think this is as necessary a condition as some people are taking it to be. So long as each simulation is simulated from somewhere, there's no reason why it can't be the case that every simulator is also simulated. I can think of no reason why the universe would be like this, but I can also think of no reason why it can't be that way.