Just re-read your #10 post. I think you said it in reverse.
1- The inner shaft , smaller diameter with smaller # of gear teeth is actually your PTO drive shaft. It couples with your flywheel gear. Through a counter shaft that torque is sent to clutch pack. Clutch pack is normally not engaged and is monitored by a safety switch so most probably you cannot start the tractor with PTO engaged. Any time the tractor is on the PTO shaft is turning all the way to the pto clutch pack. Your final PTO shaft turns only when you engage your PTO by the lever. There is bit of hydraulic coupling and that is why you felt the resistance. On my kubota I have a PTO brake but don't know if you have that.
2- Your outer input shaft that is coupled with clutch disk is actually your transmission input shaft and activating the transmission clutch in no way can interfere with rotation of pto input shaft.
On , transmission driven PTO like my Ford, I have only one input shaft and it is not coupled with the flywheel. There is a pilot bearing that with the ID almost the same as OD of input shaft. I do have an internal ORC (Over Running Clutch) ,to allow only one direction on how the PTO turns and freewheels on the opposite. I have not checked with all makes and model but overall, independent PTO don't have ORC clutch.