Is the simulation just of us though? Or is the simulation of a much larger portion of the observable universe? We naturally want to be important, but I don't see any particularly compelling reason to think that we are. I don't see any reason at all to assume that if we are in a simulation, it is being run by anything remotely resembling us (or used to resemble us), or indeed by anything at all.
Is that such a strange concept? The prevailing school of thought, if the universe is not a simulation, is that there is no mastermind behind it. Seems natural to me that we would assume the same about any universe simulator.
That made me thing of a tangent - could the incredible distances between stars and the relatively slow speed of light be intentional, a way of preventing the simulation from grinding to a halt if any of the intelligences ever learn how to travel in space?
Maybe there's not enough resources to completely model everything we see in the sky, so there needs to be some mechanism to throttle exploration.
It seems to me that's kind of the defining feature of a simulation. If there's no one behind it, if it just exists entirely on its own, then it is the natural universe, not a simulation. Even if it looks computationally-based, that's just The Unreasonable Effectiveness of Mathematics at work.
A simulation means "someone made it". They may not be masterminding details of our lives, or our civilization, or even our solar system if they only happen to care about something completely different from that and incomprehensible to us, but nevertheless calling it a simulation implies that a creator at least exists.
You are just pulling that concept from the traditional definition of "simulation", but there is no particular justification for doing so.
If we detect evidence of what the author of the paper is calling a "simulation" (that is, our universe is being simulated in a 'meta-universe'), then we know only one thing about the meta-universe: It can simulate ours. We don't know that it supports some sort of "life" of it's own, contains anything with "intent", or contains anything like that at all. We do not know that there are meta-men in the meta-universe.
Perhaps there better terminology for such implications than saying a 'meta universe is simulating our universe', but the fact that we are using that terminology in the meantime does not mean it is reasonable to make the assumptions about it that you are making. Just because we call our universe a "simulation" does not mean that there must therefore be meta-men.
(Also I do not understand the point you are trying to make about it being the "natural universe". If some sort of meta-man made a simulation that we live in, instead of the simulation arising through non-deliberate means in the meta-universe, is his meta-universe any less "natural"? Either way the meta-universe is "natural"; whether meta-men exist or not)
In a nutshell what I am saying is that we should not assume intent unless there is evidence for intent. Evidence for 'simulation' itself should not be misconstrued as evidence for intent; it would be evidence for nothing but 'simulation' itself.
Is that such a strange concept? The prevailing school of thought, if the universe is not a simulation, is that there is no mastermind behind it. Seems natural to me that we would assume the same about any universe simulator.