Let's do the comparable comparative work on cilia that has been done on hemoglobin, and my prediction is that we'll have be able to imagine the evolution of this system much more readily. In fact, I would suggest that he mocks the efforts. Time will tell. I think that Mike would disagree with your assessment that he is only arguing against gradualist Darwinian explanations, even though that is his main focus. In the book he makes the point that Darwinian evolution is the only kind that is widely accepted anyway.
Nothing is neutral in creation.
All that is demands a religious response and we either worship God or we commit idolatry. I am working on expanding this article in a review planned for some journal. I hope to deal more specifically with some of Mike's examples. In this paper Terry summarizes Mike's arguments and then responds to them. Good and well.