I sometimes envisage the simulation as the random by-product of some other computation. That we exist in the noise, the margins of some extremely large (maybe "game-of-life"-like) computation. The runners of the computer computation don't know what is happening at our level, they just see the underlying binary representation and the eventual result. There can be a large stack of emergent patterns, from the bottom-most jumbling of zeros and ones to quarks and eventually atoms and molecules. Even if they are looking at molecular level they would have no idea that anything alive and conscious and suffering is in there. Just funny moving patterns! How could they recognize a completely alien ecology running at arbitrary speed?
A somewhat scary thought.