I'm going from memory here but I believe what you suggest is possible. The aluminum plate is drilled and tapped after the hull is constructed so the holes should go all the way through. If you want to go this route, I recommend installing a port so you can see the inside of the hull.

Also, you can try e-mailing Matt Miller at Hobie Cat USA. I'm sure he has seen this problem many times. He visits this BB but an e-mail may be quicker.