I had this job re-inspected and a different inspector came out. The first one is an unpleasant man with whom you can discuss nothing. The 2nd one explained that Denver has basically made an arbitrary ruling about how to handle this situation. It is not written anywhere but they will allow NM to enter an enclosure but not to pass through anything else. We pointed out to him that if you go to the UL site it states that the conductors are essentially THHN (thermoplastic, nylon, heat) and questioned why a stripped cable, which is now essentially a set of THHN conductors, was not allowed to pass through. He stated that if we could get the UL spec's along with the manufacturer's spec's that they (at least he) would take this into consideration in the future.
It seems that even a largish city like Denver still plays the game of "it's not in the book this way but...."