What difference does it make? Dembski would have you believe that the only way to disprove the irreducible complexity of the flagellum is to show, in great detail, the exact evolutionary pathway that created it. But why on earth would I bother with that? The TTSS is a perfectly functional subsystem of the flagellum, meaning that I can obviously take parts away the flagellum and have a useful structure left over, which I'm not supposed to be able to do if the flagellum is really irreducibly complex. Whether the TTSS came from the flagellum or vice versa really doesn't matter at all - one is a functional subset of the other, where the other isn't supposed to have functional subsets, by the very definition of "irreducibly complex".
You mischaracterize the argument. The function in question is mobility, not transport of virulent proteins. And function is the determining factor in why it is not irreducible. A watch used as a paperweight is not irreducibly complex. When used to tell time it is.(note: that is not to measure time).
The fact that copper and sand are useful does not make the Pentium IV reducibly simple.
Years ago I was watching one of the last shows of the William F. Buckley. Jr. debate series on PBS, The topic was evolution vs. creationism. He had on his team an amazingly and disappointingly annoying man who repeatedly argued every point that the evolutionist team brought up by saying 'show me every step.' If every single step of evolution in fossil record could not be shown for an animal, he would immediately say that the process could not exist because steps were 'missing.' It didn't matter if work was ongoing or that million year old fossils are hard to find or anything. If every single step could not be laid at his feet, then the thing did not exist.
A woeful injustice to logic and thought and to the quality that I had come to expect from the series. Yet, it is a tactic of the creationist argument to expect.