Welcome to stackexchange. I'm not exactly sure I understand your question, but I think I do. Have you considered attaching it with machine screws? Maybe you can attach/detach with wing nuts or star knobs?
I've actually done something similar with my crosscut sled on my table saw. I have a piece of 1/4 in ply in the center where it meets the kurf. I switch it out when the blade deflects and no longer is a zero clearance slot. As long as the machine screws are far enough from the blade, you only have to cut a few holes once in the MDF (and of course, matching holes in the 1/4 ply) and you don't have to cut any more holes.
Edit: Based on your comments, it sounds like you need a t-nut in the mdf side and a machine screw on the plywood side (countersunk in). Then you won't have any hardware getting in the way.