Your splines look good, it's obvious you have maintained them well.
Can you detect any free play or looseness in the shafts on the engine and transmission? It is possible that a bearing is bad in the engine or transmission.
Is there a lot of free play in the shifter that results in needing a longer stroke to change gears? That could indicate a loose grub screw in the shift mechanism that might allow the forks and sliding gears in the transmission to rattle.
As far as your question, when the clutch is engaged it transmits rotation and torque to the internals of the transmission, loading the gears and internal parts. This helps to reduce the rattle.
As a test, with the engine running and the bike on the center stand, put the transmission into 4th or 5th gear and spin the rear wheel up to 40 or 50 km/hr. Quickly shut off the throttle and see if you can hear the rattle. Doing this test will unload the forward loading on the transmission internals. If it rattles during this test, it might mean that there is a bad bearing or a loose part in the transmission.