So I've read a lot of theories on why this happens on various clutches (seems to be a common noise among lots of platforms).
Best explanation that I shamelessly stole.:
"A piston engine crank doesn't rotate at a constant speed. The piston movements cause the crank to keep accelerating and decelerating during each rotation, just because of the inertia of the pistons and rods. Even with perfectly balance carbs or injection, the inertial torque pulses are still there, and when the clutch is engaged these pulses feed through primary reduction gears and clutch to the gearbox input shaft, adding mass to be accelerated and decelerated too. This adds some NVH - noise, vibration and harshness which almost all disappears when the clutch lever is pulled in."
This lines up with a guy on an R1 forum who said he fixed/massively reduced his chatter with the lever out in neutral that when away by pulling the lever in by adjusting his valves. On the surface that makes no sense, but if it smoothed out the engine, I could see it. I also read about people syncing their throttle bodies/carbs helping out too.