Therefore, I reasoned that these low-level rules you're talking about may manifest upward in scale. If you created layered approximations of observable behavior, you could essentially capture the output of these rules even if not directly discovering them at a low level.

If you have a protein, a plant, planet and galaxy all on equal footing in terms of how they're approximated and simulated, then perhaps one could factor out commonality from each and deduce some sort of low-level rules from that.

With respect to our reality being an ancestor simulation, I'd say it's highly likely. You might be interested in looking at Bostrom's simulation hypothesis, if you already haven't.