I think that spot rusts also because water sticks to the bolt.  As it dries, you will see that water will remain near that bolt, which helps rust.  So what you have done is a pretty great idea, but I'll be very curious to see how it holds up over time.  As long as the paint is waterproof and the hole has all the bare metal sealed, you may just have hit on the solution to the rust problem there.  
My Genesis Silver B had rust also where the cookbox sat on it, also because the water would be there longest, and there would be water there from dew, not necessarily rain.  Just a lot of water exposure.  
Just thinking about rust.  
Did you weed whack and blow too?  Can't do half a job!