What a terrible ending to the article. What Musk is warning against is a system that is capable of accomplishing it's own goals, and if those goals conflict with our own goals then there will be trouble - especially if the AI is clever enough. Whether or not we are living in a simulation is irrelevant - we are still agents with goals.
Maybe the author was trying to be silly, but, if that's the case I can see why he writes for CNet at not Comedy Central.