References to Italian history
This movie is a Leone commentary on Italian history, especially Italian Fascism and WWII.
The gunning-down of the people in the pit (in Guadix), the massacre in the caves of (amongst the lot) Juan's family are just two examples - experts on Italian history will find a lot more, I'm sure.
The deserter being executed with his back to the firing squad looks very much like the young Mussolini - and a Leone expert (Frayling?) remarks on that. But what is more telling is that Governor Jaime - with his moustache, receding hairline - looks like a even younger Mussolini (as an editor of Il Popolo d'Italia of 1915)! I just found the picture in an old book and that picture gave me a new look on what Leone wanted to tell us with the movie: you can't duck your head forever (or should I say that you some day might have to stick your neck out for somebody else (Casablanca!!!))
No subtle hints, here: No doubt what Leone thinks should have been done to the coming Duce - preferably before he became Duce!