RE infinite regress, turtles all the way etc.:

it might be.

but within digital simulationism, which i am leery of, one consequence is that there might not be a bottom, but there is a top. eventually you hit the limits of fidelity and no more substrates may rest upon the tower.
depending on rules, it might not be possible to cognitively detect this limit (see "blind spots"). but assuming a purely digital simulationist worldview, there would be artifacts.
if you tried to split a piece of matter in half over and over, you wouldn't necessarily be able to directly expose "atoms" in the greek sense, because of system thresholds like quantum reality, fiat fundamental particles, etc., which are part of the rules of your substrate.
but there might be fidelity artifacts which could be exposed. how depends entirely on the shape of the substrate.

if this substrate contains floating point data, you might be able to detect erratic behavior, for instance via interferometry over very long distances.
if there is some sort of system for optimizing like data or like processes, you might be able to detect artifacts by deliberately doing things which might trigger state machine shifts in the simulation, like creating large empty spaces or creating highly optimizable scenarios.
you could also perhaps create a machine for making nested substrates, which depending on how high the ceiling is, how wide your available base is, and the attainable slope of nested substrates, might eventually be able to hit the ceiling. (but again, see "blind spots").
one imagines a scenario where the nested substrate computational tower of babel is constructed, and the work is halted on the distant tower's summit, but angels inside the computer falsify reports, telling the architects that it is still proceeding. no artifacts here, sir.
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