I bought a couple extra long 1/8 and 1/4 endmills for exactly this reason. I like to be at least able to make holes/markings in the factory board.
However, you might find that you get the same Z travel if you put a wasteboard on top of the factory board, and just raise the router in the mount a bit. You have about two inches or so that you can raise or lower the router in the mount for different setups.
I recently posted photos of my setup here (hopefully linky-link works):