So it turns out that you agree with me that one cannot follow the advice of the "three clue rule" and the advice to prepare situations, not plots, at the same time.Indeed, as he states in his opening sentence that you quoted, it's advice on how to prepare A MYSTERY SCENARIO (which one would expect to have a plot of some sort). It is explicitly NOT advice on how to prepare a sandbox, a Story Now game, or how to convert a tractor to run on biofuel.
Upthread @mamba, @overgeeked, and (I thought) you had asserted that the two bits of advice can be employed together.