I don't understand. How could it "over-run" the engine? The engine is already turning at full PTO speed -- the flywheel of the
chipper can't make it speed up. It always seems to me to let the engine come down to idle speed so you slow down the flywheel quicker, then disengage and let the equipment come to a stop from there. (This of course if you don't have the old setup where the PTO can drive the transmission.)
If the implement has a giant flywheel or flywheel action, it is going to hold onto it's rotational energy a lot longer than the engine, and as a result it's going to transfer some of that energy to the engine and over-run it. You know from experience an isolated engine will drop in RPMs very quickly if you cut the throttle, since it has a small flywheel and lots of friction and losses to drag the RPM down. Not so for something large with a big flywheel and minimal friction losses.
Even if you slowly ramp down the throttle, for every drop in speed of the engine, the large-flywheel implement will lag behind and be pushing the engine.
You won't increase the RPM of the engine above the RPM of the coupled implement (taking gear ratios into account). But you will most surely increase the RPM of the engine above (perhaps way above) the normal RPM of the engine at the given throttle setting.
Best example I can think of is a car with manual transmission. Get up to speed on a downhill and take your foot off the throttle. The engine RPMs will then be driven by the inertia of the moving vehicle acting through the transmission, and most certainly be higher than the engine would turn at the same throttle (which would normally be idle speed). We think of this as engine braking, but in reality the inertia of the vehicle is over-running the engine through the transmission and gearing.
So if you throttle a tractor back with a large implement engaged and turning, you are in effect using the tractor's engine as a brake to hold back the implement and slow it down. But there is no real benefit and there can be some potential disadvantages. That is why when running my
chipper, I clutch in and let the
chipper and PTO slow down on their own while I independently cut the throttle and let the engine go back to idle on its own. There is zero reason why I'd need to be using the engine as a brake in that situation.