For many reasons, I don't like the "hole through the table" idea. Not the least of which is workholding - you'll need a way to hold stuff in place - and a way to get in there to do that. Wrenches, clamps, screws, etc all need clearance to fasten. Plus, if your gantry is a closed loop, you would be restricting what moves can be made while something is mounted in that hole (i.e. if it has a bottom crossmember (which would make it very rigid), it would not be able to travel past your board sticking down below). Doesn't seem like a big problem, but could be.
I very much prefer the "hang off the end by 3-4 inches" style for handling vertical boards.