I don't see how an upside down piston ring would cause oil to collect in the combustion chamber while the bike is not running, resulting in a big puff of smoke on startup that quickly goes away and heavy deposits at the intake valve. I doubt you will ever get a factual story from that dealership, and as long as you get the bike back this time in proper running order I guess their little story to save face is just water under the bridge. I hope everything goes right for you this time.
Btw, a real engine builder would know which way to install the rings even if they weren't marked. If the gentleman putting your engine back together didn't find the directional marks and he doesn't know how to tell the difference, he should have stopped at that point and found out for sure.
Jerry