Is I see it there is no need for alignment like in 4-strokes, regarding to timing of the cam, but needed when it comes to "balance". The clutch will spin pretty fast, and if it is not "balanced" together with the crank I guess there could be some nasty vibrations. Maybe the "unbalance" of the clutch is supose to take away the "unbalance" of the crank. Most single cylinder engines has a balancer shaft, maybe the clutch on the NSR corresponds to such a thing...(seems strange though since the clutch wont spin with the same frequency as the crank).

If everything was balanced directly from the factory then there would be no need to align, so the white spots must mean that the clutch is not perfectly balanced. At least thats how I think.
_________________
MC21, GP-Replica (Daijiro Kato, Telefonica Movistar Team 2001)