Not a great picture but in mine the holder protrudes about 1.5" to 2" through the top of the rod box and to a lesser extent through the rear. It pretty much drains into the cockpit and a little baffle work could ensure that it completely drains into the cockpit. It sticks too far down to use a shim on top of the gunwale IMO but maybe you could split the difference with a 1" shim and trim an inch off the bottom of the holder? Maybe just trim the lower corner off of the holder or maybe move the pin up some too and then cut a bit more off. Note that if you don't cut the rod box, the holder will drain 100% into the hull liner so covers or drain tubes will be needed.
