POPE also refers to whom ever is in charge of JSOC AT ANY TIME.
Eikenberry's beef with McChrystal goes back to the time when McChrystal was the Pope. The Pope is the head of the Joint Special Operations Command. The nickname goes back to an off-hand remark that Janet Reno made after failing to obtain information from JSOC after the raid at Waco. (JSOC operators were on the ground to keep watch on their equipment but did not assist in the raid itself.) She called JSOC the Vatican. And the head of the Vatican is … the Pope.
Sauce: https://www.theatlantic.com/politics/archive/2010/06/the-night-beat-what-the-heck-was-mcchrystal-thinking/58480/