Re: 929 shaaaaakkkkkeeeess...
I agree that if the rear wheel is misaligned, you might see the symptoms you described. Under power, the shudder might show. While not under power, you could just see it lose extra speed while coasting, but with out the shudder. The more scuffed wear on one side is certainly a stand out symptom. That is unusual.
Did your old tire show that one-sided scuffing at all? How many rears have you run though so far? When checking alignment, are you just checking to the swingarm pivot? Maybe you should check all the way up the the front wheel. Maybe the frame has a problem? Was it dropped before you owned it at all? Could there be a problem with the swingarm bearings? Can you suspend it so the swingarm is dangling and check for freeplay?
BTW, the chain alignment markings on my 929 do seem to measure out as accurate. I suppose your's could be different.