I think that "on top of" is meant metaphorically, as in usages like "the apartment was small so everyone lived right on top of each other". This can be contrived to make a sort of sense if the author (of that anecdote) had been planning to either sneak a peek at the notebook without Gates noticing, or suavely open the notebook "let me check my notes"---which is trickier if you have to say "let me check my notes, if you'll move your elbow, excuse my reach, thanks". Note that the notebook was "on the desk", so sitting actually on top of it would be strange.
But I agree that physically "on top of" the notebook was the first reading I had as well.