If we are in a simulation, all of our logic will not be universal but instead will be a reaction to the perverted rules set up by the simulation's creators.

While I do not agree on the conclusion of the simulation argument, I think your rebuttal is flawed: we can safely reason about the reality outside simulation if we presume that we are inside a realistic simulation, that is a simulation whose purpose is to mimic as closely as possible the reality outside. I don't know if it's made explicit in the exposition you read, but I've always assumed the argument was about a realistic simulation. Indeed, if the law of physics are computable, you can have even have an emulation argument.