I had this too. The leak seems to be behind the lights, took them out and resealed to no avail. Has to be higher up so suspecting the roof rails. They have no holes or areas which could leak so the only place was the end of the roof line directly below the black gutter stripwhich you look at with the tail gate open.
There was a post recently on this which showed a hairline crack on the 'fold' at the rear end of the roof. Ford wanted to dig the old sealant out, redo and respray. Huh. I used some nail hardener!, Don't know if this short term cure still works as I have traded the car.