I had removed the bolt on PTO shroud on my JD650, for similar reasons. Then, in my capacity as a volunteer firefighter, we were paged out to a "severed hand" call. Well, it wasn't severed, it was just pulled off in pieces, right past the wrist. He had a winter mit on, touched PTO shaft end that he didn't notice was turning, wrapped up the mit, and the trail of blood lead us to where he was sitting at the house. I had the job of unwrapping the mit from the PTO shaft, but nothing usable in it. I went home, and the first thing I did was bolt back on the shroud over my PTO shaft. It's just me, but that was my message in life about PTO shafts, and guards. All my shrouds are in place, and my PTO driveshafts have working spinny things on them.
As a side note, the flip up shroud on the JD1025R, when properly lowered in place, also holds the pins in place for the three point arms.