Interesting research here. Not directly attacking the “Are we in a computer?” question, rather, looking to see if such a computer could be built.
If it is possible, odds are fairly good that we are not in the original universe.
Confirming this for sure, or determining how far deep we are, is still looking fairly unlikely.
This could be an interesting Matrix IV concept- Neo was in fact in the “real world” of the human-robot war at the end of the series. He was not in The Matrix. But… that “real world” was running in a computer in a lab somewhere and had been for billions of simulated years. Noone, not the robots or humans featured in the first three movies, The Animatrix, the Matrix Online, or any other related material, had the slightest clue about this, anyone who suggested it shot down as a crank. It explains away some of the parts that went off the rails without destroying entirely what the heros had fought so hard for.
“Damnit Bob, that simulation is going wonky again” “Just hit the one button Steve, it should get back on track in a few minutes” being the potential closing lines.