Modern sportbike rotors are usually 4.5mm thick. I'd bet our moto brakes are real similar. Don't know what kind of caliper you have, but I suppose you're right that the hydraulics would compensate. Use an old pad backplate, and a C-clamp to push the piston all the way in the caliper, then put your pads in and try. I've raced a superbike, where we had to shave just a little thickness off the pads so they would fit, and not drag. Other than that, they worked fine.