I don't use an Adjusto-Jig - I just use 5/16" CF rods on blocks on my flat building board.
But since I scratch build, I just design the cutouts to miss the jig holes, or if a cutout must be around a jig hole I only partially cut it out, so that I can finish the job in the wing with a couple of flicks of the X-acto knife.
(What size are the Adjusto-Jig rods? If they're 5/16" or thereabouts, get a matching Forstner bit on Amazon. You'll be happy you did -- it makes much cleaner holes than you can do with anything home-brew).