well try not to be fallible too often! :)
I like the glueing idea, but without its metal baseplate the nut is too low. So I could shim it, but what would be suitable and glueable (wood obviously, but I don't have a spare piece of maple or similar).
At the moment I am slightly veering towards filling the holes as you suggest, redrilling through the neck, bolting from behind with the bolts slightly recessed into the neck to they are flat and out of the way. The thread of the ebanol nut should keep it in place, but that is a bit of a sledgehammer to crack a nut. (This bit was supposed to be easy - I still have to drill the holes in the neck to attach it, and redrill bridge holes to fit new VS100 :( )
Cheers