The difference is that there's an underlying assumption that base reality is analog and perhaps continuous rather than discrete, and definitely not CPU or memory constrained.
In the scenario you mention, reality would be a program because it is still run on a computer in either case. If reality isn't a simulation, then we shouldn't be able to DDOS it, or overflow it, crash it, access a memory buffer, get root access, or execute timing attacks as those things are artifacts of computation.
Let's assume mankind could create a machine that could crash the universe. Should we ever press the button to test it? And if the button is successful (the universe terminates), how would we get to know the result of the experiment?
In the scenario you mention, reality would be a program because it is still run on a computer in either case. If reality isn't a simulation, then we shouldn't be able to DDOS it, or overflow it, crash it, access a memory buffer, get root access, or execute timing attacks as those things are artifacts of computation.