Note 1:
No. It’s being set up as a continuum: That there are some IC systems (IC version #1) that are accessible to evolutionary mechanisms and others that aren’t. If a possible explanation for system ‘X’ is made, one can always move on to system ‘Y’ not being explained. I don’t find the bacterial flagellum a particularly enlightening test case.
I believe that for most systems, the requisite signal or remaining evidence will make it impossible to trace historical pathways in any great detail. Signals decay with time. The bacterial flagellum is ancient and highly evolved. Personally, I’m surprised that there seems to be some links to secretory systems. If I wanted to test the limits of a hypothesis about ‘evolvability’, that is not a system I would consider tractable or likely to achieve conclusive evidence. In contrast, the blood clotting cascades found in mammals are younger and there seems to be more discernible connections, particularly with replication of proteases in the cascade. But even there, Behe asked whether the models could predicted whether changes in the components could modeled with terms including blood clotting times, clotting thickness & permeability, and not clotting under inappropriate conditions. Note: This is a level of detail we don’t even have for extant models of clotting cascades, so it’s unlikely any model of the evolution of the blood clotting cascade will come up to Behe’s level of request for quite some time. Color and scent receptors are also systems where enough data could be retained to evaluate ICness and evolvability, but again, possibly not likely at the level of detail Behe might request.
In actual science and determining the applicability of a hypothesis, researchers tend to investigate the simplest cases with the most likelihood of returning a positive results. So, what is the most recently emerged system for which we are likely to have sufficient data to discern evolvability? It’s not the bacterial flagellum.
Note 2:
It’s a queer asymmetry of logic that defeat of Behe’s IC hypothesis requires proof of evolutionary pathways. Ultimately it reduces to: “I might be right as long as you don’t prove me wrong”. That’s the problem of setting up a hypothesis as the negation of another hypothesis rather than as a positive argument. For example, the evolutionary hypothesis leads us to suspect is that connections of linear descent may be found between past and present organisms. What is the positive formulation of the IC hypothesis? Can it be formulated or evaluated independent of whether an evolutionary mechanism can be found?