I don't have any John Deere tractors, but I do have a nice collection of Craftsman tractors. I have one that's a parts rig, 42" deck, 6-speed on the fender, 14.5hp twin, (deck, steering linkage and deck lift were all trashed when I got it) and it has the keyed shaft for the rear axle. I have an older silver tractor, 42" deck, 6-speed in the middle, 18hp twin, and it has the keyed rear shaft axle. Then I have a newer Craftsman GT, 50" deck, automatic hydro, 24hp twin, and it has the bolted on rear wheels.
I've had to remove the rear wheels on all three at one time or other. Given my choice, I'd rather deal with the bolted on rear wheels. Even though the tractor was a bit neglected when I got it (with only 40 hours on it, lol), the rear wheels came right off when I pulled the lugs. The other two tractors, I pulled the retaining clip and fought with the rear tires for a good bit of time because there was a little rust that had gotten in there or they were dry as a popcorn fart.
Looking at the rear axle of the GT, it looks kind of like the spindle that the lugs are on is mounted to a keyed shaft, so I'm guessing that it's not really any stronger than a keyed shaft, it's just easier to take the tires on and off. I've been half looking for a set of spindles that will mount on a keyed shaft to convert my other tractor over.