Once you have the CVT cover off, the clutch bell should just pull off. Mine did. The bearing in the CVT cover and the nut hold it on, once those are removed, there shouldn't be anything else holding it on. Only thing I can think of is the clutch shoes are pressing against it or the splines might be damaged. If you can hold the clutch bell with your hand with the engine off, and turn the rear wheel, then the clutch shoes are not holding it.
"I was merely investigating the noise under a controlled environment" That is what I have been trying to say. Don't ride the scooter with it off. But it is ok to run the engine with the cover off, as long as the proper precautions have been taken. On a Vespa, you do need to install a spacer (maybe a stack of washers or a nut of the proper size) between the clutch bell and the nut to take the place of the bearing in the CVT cover so the clutch bell is held on properly. This is ONLY for test purposes, so you can observe what is going on under the cover. That bearing in the CVT cover is there to hold the left end of the rear shaft in place.
As for crankshaft end play, I wouldn't think there should be enough to notice, but that could be wrong. I have the GT200 service manual, I can check to see what the crankshaft end play should be, IF it is listed. Is there any radial (side to side) play in the crankshaft? I have never had a Vespa engine apart. But all crankshafts have either a radial thrust bearing, or in the case of most car engines, several radial bearings and one thrust bearing, to control both end play and radial play.
EDIT: Crankshaft end play is listed in the manual as 0.005-0.015 in. Not very much at all. If there is obvious endplay, there is likely a problem.