My guess with that sound (mine makes it too, 110k on the transmission, with 10k since I re-did the seals and inspected the internals) is that it is lash in the gears, made noticeable due to the lower RPM and therefore wider spread power pulses. When a cylinder fires, a jolt of toque goes through the transmission, and then after the initial power pulse, the momentum of the gears makes them continue onwards at the peak speed of the engine, until the reach the end of their lash, and are jolted to the slower engine speed. Since it is in neutral, all the gears are still engaged and spinning, but are not locked in their shafts.
Pulling the clutch on a BMW totally unloads the transmission due to the dry clutch: on a wet clutch bike, it would continue to make the same noises. On a BMW, the transmission will be totally stationary.
The noise disappears with load, as the impulse damper (in the transmission) takes up the intermittent torque peaks, and the transmission is loaded with forward acceleration.
If you put it on the center stand, and pop it into first, you should probably have the same sound, but amplified as the engagement of the transmission increases the inertia of the drivetrain.