Consider a matrix-like world, where the Universe is simulated on a classical computer (classical computers can do everything quantum computers can do, if slower). Would you deny that simulated humans can think and act rationally, only because the simulation does not include quantum mechanics? If not, would sim-EY not be able to write the Simquences (less the QM Sequence) which are identical (modulo QM) to the ones here?

You make a compelling case that the reference to QM in the sequences is at least as arbitrary as the fundamental physics of our universe. I'm not sure that this is quite as compelling and incisive a revelation as you believe it to be, especially to those who take Occam's Razor as seriously as Eliezer advocates. I'd actually say that this weakens your claim and that it would be better to argue, as Tim does, that the points Eliezer is trying to express don't come across nearly as well as they could.