Yes, centering can be difficult with the "cheap & dirty" methods I use. One has to poke, drill & cut carefully. I have only done that with webcam lenses--in order to prevent washing out in bright sunlight on snow, etc., and like Bill W said, I just stuck the disc to the front of the lens.
I have no experience with spacing from the lens but I expect the new aperture has to be rather close to the surface of the lens element, so if your lens assembly or iris assembly is such that the iris cannot be within a mm or so (??) of the lens surface the window might indeed be the more viable option.