Another possibility is that a gas station pump was missing or had a defective filter and allowed gunk to be pumped into your tank.
That did cross my mind, but it would seem to be very improbable that he would fill up from a source that had this kind of problem. Possible, but not likely. This adds unnecessary complexity to the explanation which violates the Occam's razor principle. That's not to say that it could not happen, but the odds get longer when you add that kind of thing to it.
I was thinking that maybe the debris entered somehow through the vapor recovery system. Was there ever a time when a vent hose came loose or anything like that. I can't remember if he has an auxiliary fuel tank, but it could be related to that installation if he has one. Driving off road in dusty conditions with something like a loose or disconnected fuel tank breather hose could allow sand and dust to enter the tank. A loose hose or other open port should have triggered the CEL and i don't think that happened.
One thing that bugs me about the dealer's approach was that they seemed to have overlooked checking the fuel rail pressure. A low or fluctuating pressure reading should have tipped them off to the source of the problem right away. I think that dealer should reimburse him for travel expenses, air fare etc. It should not have taken this long to diagnose and fix the problem. I think I could have gotten to the bottom of it much faster, and I am not a pro mechanic in any sense. IIRC, you can get to the fuel pump through a port under the rear seat. I think you may even be able to replace the pump without removing the fuel tank. What took so long?
My money is still on the vandalism theory. The gas cans are high on my list of suspects. I would check those cans to see if there might still be some debris in them even if only a tiny amount. Just playing detective here and this is all purely speculation, nothing more. I could be way off base with this reasoning.