I remember reading an article Ron Covell did in his "Professor Hammer" column in Street Rodder years back explaining this, I have also noticed this on lots of beautifully painted cars.
He stated that the added thickness of a lapped seam will cause the outer body metal to expand and contract at slightly different rates, this is more prevalent when the car is exposed to high temperatures.
I have also seen this on shaved door handles as well, since some guys simply will mig weld in a patch and leave the stamped surround lip in place rather than cutting it out and butt welding in a piece.
I make sure that all outer skin body metal is the same thickness. Im a bit superstitious and will try to sand down the back side of the weld flush if I can get to it as to not add any additional thickness to the metal.
Just my two pennies
