What he's overlooking in that desktop metaphor is that there are people who understand ALL of the inner workings down to atoms. No single person has it all in their head, but the software was written by human minds to run on hardware created by human minds that understand the device physics down to a very low level. A user of the software doesn't have to have a full model of the reality - in fact that was the entire point of the desktop metaphor, to make it simple for people so they don't NEED to understand it all in order to use it. For most users that is sufficient level of understanding, and if everyone took the full deep dive we would indeed all be eaten by tigers. But that only says none of us has a full model of reality, it does not say our model of reality is wrong in any way.
I find it amusing that he chose a metaphor designed to hide the complexity of reality from people while ignoring the fact that it was done that way deliberately by people.