Some of this is just annoying semantics because people use the words BOTH ways when referring to a clutch. A clutch is technically something that DISengages something. If you just took a clutch assembly out from between two shafts and replaced it with a coupler or made it one shaft it would just be engaged all the time. So a clutch DIS-engages something. By extension you could make a statement like ENGAGING a clutching mechanism, DISengages the driven mechanism (like a pto shaft). Which is super confusing. And sometimes that's why statements using engage/disengage when referring to a clutch, can be inconsistent and confusing compared to other similar statements.
But..
My guess, is what is meant in THIS CASE, is just 'dont ride the clutch because you'll wear out the throwout bearing', which is just generic clutch pedal advice that applies to cars and trucks and other things with clutch pedals and throwout bearings. I don't think it specifically means anything about the PTO itself, just saying don't stay on the pedal for a long time because you'll overheat the throwout bearing and start wearing the tips off your pressure plate diaphragm spring fingers. Just regular old 'how to drive a manual' tips.
The reason why you would even have to make this statement at all, comes down to 'live PTO'. Because in a car you're not going to hold the clutch pedal down for THAT long because the car won't move! But in a tractor you could have a clutch BEFORE the transmission that also disengages the pto, or you can have a clutch just for the pto that won't stop the tractor from moving. So in a tractor its possible in some cases to just push a clutch for a pto, and then cruise around like that forever because the tractor will still move! So i guess someone HAD to say in writing 'hey don't just ride that clutch forever or something bad will happen'.