The solution to the Watcher's arm problem is simple:
The Watcher has two left arms.
This isn't totally delusional. Characters in Mythworld have all sorts of weird traits, and compared with some of them, having two left arms is fairly reasonable. The Watcher has two left arms, and we have just never considered that possibility.
I doubt, if this theory is really the tru7h, that it has anything to do with the plot of Myth, and is only a cynical diversion on the part of the Bungie team. But who knows. . .