The over-riding clutch (ORC) is what Kubota calls a slant cam. I attached a drawing of it. When you reduce the throttle the implement keeps the PTO shaft turning while the engine slows. The slant cam ratchets under these conditions to prevent the PTO shaft from over driving the mechanism.
You'll notice that as soon as you reduce the throttle you hear the ratcheting noise if you have a big implement attached. What I do is to slowly reduce the throttle and and then disengage the PTO as soon as I start to reduce power. Under these condition the slant cam is unloaded and beginning to ratchet. If you pushed the clutch in you would have the same condition only it would happen much faster and noisier.
I actually started by pushing in the clutch and then disengaging the PTO real fast so the noise didn't last long. Then I decided on closing the throttle instead of using the clutch. I use my left hand on the throttle with my right on the PTO lever.
This noise should not really hurt anything but it is annoying. I always associate noise with wear but I think the wear in this case is so slight it would never hurt anything.
You NEVER want to ENGAGE the PTO wihout the clutch. It is also important the clutch fully engages when you enable the PTO. If you notice the PTO lever binding or getting harder to engage, have it taken care of right away.