We can make a simulation today, and have it obey such natural laws (of course programmed behavior) + logic (ditto), so that we could encode whatever we want inside a physical or geometrical constant as it appears inside the simulation.
Huh? It's trivial to do so. You just give the simulation the appropriate algebra that applies to all their measurements.
Not more difficult than setting 12=66 to programming languages that allow it (there are some, it can also be done in others like Python through some trickery [1]), and thus changing all the subsequent calculations done there.
[1] https://www.reddit.com/r/Python/comments/2441cv/can_you_chan...
Yet somehow a case is missed out, and some day someone asks the VM for pi in some other way, a discrepancy is found, and there you go...