Most likely poorly balanced throttlebodies or someone has messed with the throttle stop screw trying to lower the idle.
Throttle body balance is very important. The thing to remember is that crank speed is not constant. It will speed up on the power stroke and slow down as a piston comes up against compression. On a 90 degree twin with a shared crankpin this issue is exacerbated by the uneven firing intervals of 270 and 450 degrees and if one cylinder is working harder than the other it will be even more pronounced.
What is causing the rattle when the clutch is not engaged, (Lever released.) is that the input shaft and primaries in the gearbox are accelerating and decelerating with the crank and the 'Knock' is the backlash between the gears as they biff against each other first one way and then the other as the crank speeds up and slows down.
It's another reason for the slightly higher idle than in previous engines. The comparatively light flywheel, (Which is essentially a 'Battery' for kinetic energy.) doesn't do as good a job of smoothing out the power pulses of the bigger, higher compression, cylinders/pistons. If it ain't set up right it'll rattle like a bastard.
Pete