There's a fairly simple explanation, when you think about it.
They arranged to have the simulation in our universe turned off, but not to have all simulations turned off -- there's no way they could do the latter. So they ended up in a simulation run by someone who'd started off by simulating Earth, and who -- more likely than not -- were especially interested in embedded simulations.
Embedded simulations like theirs, but also like the Autoverse, and whoever it is was interested enough that they'd violate the simulated physics of Earth to keep simulating the cellular automaton despite the physics of Earth saying it should be shut off.
Viewed from that perspective, the ending is... not predictable, exactly, but at least plausible.
They arranged to have the simulation in our universe turned off, but not to have all simulations turned off -- there's no way they could do the latter. So they ended up in a simulation run by someone who'd started off by simulating Earth, and who -- more likely than not -- were especially interested in embedded simulations.
Embedded simulations like theirs, but also like the Autoverse, and whoever it is was interested enough that they'd violate the simulated physics of Earth to keep simulating the cellular automaton despite the physics of Earth saying it should be shut off.
Viewed from that perspective, the ending is... not predictable, exactly, but at least plausible.