May be these ATmega16U2 have some pin;s open and freely usable but hardly they would be used as not many would be messing with the Bootloading code, these guys are messing with the Simplicity of the Board.
i remember one post back where Nick posted about Rev3 pin-outs saying that these headers have made it further hard to use that mounting hole as this was the only hole because the other one parallel to it is already filled with Caps and power jack making it very hard to use in mounting.
Moreover these new changes must be clarified by the Arduino team this is not the way , if the forum is filled with pretty much experienced guys this doesn't means that they gonna shed the responsibility on forum;s nice guys.