Re: What is this hole doing there?
That's where they sprinkle the magic fairy dust in the Custom Shop models.
True story...when Fender took apart SRV's Lenny for the relic re-issue, they found several small holes under the pickguard where Rene Martinez had cored out little sections trying to balance the weight of the instrument from the left handed trem. The small hole also created a better moment of inertia to balance the force of the heavier strings that Stevie used. All of the holes had been filled back in except the one that is in the same location you are seeing now.
Okay, maybe it isn't true. But it would be a cool story.