I don't understand what this issue is you warn of?
It goes up and down with a spin of the wheel.....and you can move the deck up and down to reduce or increase the gap between the drill bit and the wood.
I thought that to drill string through holes you would just adjust the deck height so the wood fits. Put a small drill bit in.....drill through.....flip over the wood and put a larger drill bit....depth marked....and drill the recess for the ferrules.
I don't understand why this drill press would not work? The body wood is 40 to 60 mm thick, surely it can move that far?
But there isn't enough distance from the upright to the drill bit to reach the bridge area for string-throughs. It would be ok for tuner holes and other holes that are closer to the edge of the wood.