Derek,
I just don't see how you are getting what you are explaining out of the citations you are giving.
I tried to point at the disconnect by the hypothetical NM looped in a metal j-box. You responded that, based upon what you are reading in the NEC, the NM EGC wouldn't HAVE to be bonded to the metal box, however, in the field you would bond the EGC.
When I read 250.86 and 314.4, I read that the EGC must be bonded to the metal box, except for Remote-Control, Signaling, and Fire Alarm Circuits, as described in 250.112(I)