I've always wondered if perhaps Lee Falk or Ray Moore didn't at the beginning think of the "good sign" as the crossbones from the pirate symbol Jolly Roger. The Phantom had already adopted the skull as his emblem, and since his origin was tied in with piracy, I suspected that he might have been intended to be shown turning pirates' dreaded symbol back against them. But I've never seen this in print, it's just one of my many many skewed theories.