^^^ This. I have two MIM Jazz basses - a Geddy Lee signature and a fretless. BOTH have this hole under the pick guard. When I first noticed, I looked it up and the consensus was a hole used or made by the CNC machine. I would keep the pick guards on mine anyway, even if the hole was not there, but I'm sure it's frustrating to someone who wants to remove the guard.Without seeing the hole you're referring to, it sounds like a guide hole used for the CNC machine cutting of the body at the factory.
