What are your thoughts on these scenarios?
It sounds to me as if you practice 'good' PTO engagement., (you engage at low RPM then slowly bring up to operating speed.) It is Extremely unlikely that something is broken.
However, bearings can 'go bad' at any time. (especially if their lube is overheated)
When I used to help out on the family dairy farm. They had
HUGE JD tractors (all 4 wheels over 6ft tall...the rear wheels were dual on each side) they ALWAYS engaged at low RPM and slowly brought speed up. When you are talking about 100s of horsepower driving a corn-chopper, it is all too easy to
twist a PTO shaft if care is not taken. (A corn-chopper takes 8ft tall cornstalks, chopps it into fingernail size bits then blows into dumptruck running to the side.... it is not hard to envision how much power this consumes with a 20ft swath.)
I took it to the dealership yesterday and the mechanic hooked it up to the dyno and discovered the wobble.
It is encouaging that they were able to duplicate the vibration. I understand that it is not easy to diagnose without some disassembly.