The counter point, for me, is that's a very complicated way to produce the universe we actually live in. What is the purpose of the simulation? Is it to be similar to Conway's "Life", in which case why build something so convoluted, and why cheat as apparently the programmer did with 2 and 3?
If not, if the aim was to create sentient beings (well, me at least, I can't speak for you idiots), then, again, why create a system that requires fourteen billion years to actually produce them, with them being around for a mere 50,000, and each having a life span of (almost always) less than 100 years?
And if you're about to argue the universe was created ten seconds ago, well, no, because there's apparently information in it covering about fourteen billion years. To ensure the system is stable, the logic and current state has to fit that fourteen billion years AND has to be stable right now. One off-by-one error and the Earth will go spiralling into space, or get sucked into the Sun, or just disintegrate, or turn into a black hole for a split second, or...
I can explain why John Carmack created a number of "virtual reality" (Doom and onwards) games, but he didn't create some overly complex physics model, just the bare minimum to work for the observer. Our universal engineer, however, appears to have created this enormously convoluted system for no apparent reason. I'm not seeing the reason to assume intelligence when a more likely reason for the things you note is that our universe is more complex than you want to believe it is.