The mounting bolt could be bottoming out, so you can cut 2 or 3 mm off of it, no harm done, but then you have to make sure that the cut end is nice and flat and tapered so that it can engage the crankshaft threads easily and correctly, I always add a lockwasher, it's an easier solution.
Also, you can use use your Dremel tool to slightly enlarge the taper on the CC, or turn down the crankshaft slightly.
Don't hammer it, you don't want to cause any damage to the bearings and possibly oil seals on the crankshaft.
Perhaps the easiest solution is to make gaskets to take care of the spacing gap of the small cover, then you can go out riding and enjoy your new centrifugal clutch, and take care of the final fitting at a later time at your leisure.