We know that your "some natural processes did this for some reason" is a straw man because we know that nobody regards such as a valid model. And I have shown that in a particular case loved by the ID movement we have FAR more than that.
Of course if you reall wanted to dispute that claim you could have backed it up when you had the chance - instead of producing a clear example of the double standards of the ID movement as you did.
Moreover the argument that you call a "double standard" is nothing of the sort and in fact is prefectly valid. The information needed for a bacterium to build a flagellum IS encoded in the genome - ergo if the flagellum is to be held to be "designed" at all this must be the intent of the designer. How the designer arranged for the information to get there does not change the fact that the designer must have done so somehow.
As for your comments on homology, please identify the structures you are referring to and explain the roles of the genes involved in each case - in a different thread, since such a large subject deserves a thread of its own. I certainly don't intend to do heavy work on developmental biology and genetics to answer such a vague request especially as even if I were to do so for a single example (which would be a lot of work in itself) you'd probably find some excuse to dismiss it.