Where are they misleading? It is of interest.
The moral of the story is that the specification you're testing must be independently derived from the result. It is his parable so clearly he understands it. Yet here he is asking about some probabilities with no independent specification.
He misleads in other ways too. Even if one were to (illegitimately) accept the flagellum as a spec, one can't ask only about the probability of some specific sequence of changes but must rather ask about all the conceivable evolutionary pathways that could give the result. The man is a mathematician, he knows his question is misleading.