I always assumed that "Endless Deep" was an experiment left over from the October sessions. That lyric, "Where do we do from here," perfectly echoes the opening of "With a Shout." It also is reminiscent of another October track, "Is That All?" because both come across as questions U2 is asking itself.
It's possible U2 dragged "Endless Deep" out for a "War" single because clearly there was a shortage of material for B-sides ("Treasure" was the only other War-era B-side that was a new song.)