Before you go cutting the PTO shaft, you need to make sure that it is in fact too long. Before hooking up the arms and the top link, (with the tractor close to hook-up position), attach the PTO shaft. It slides in and out- pull it out enough to hook up to the tractor PTO shaft. Then, pull the tiller forward enough to hook up the arms and the top link. At this point, there should be some forward and backward movement in the shaft. If it is tight, then you need to cut the shaft down some. Slowly raise the tiller, watching the shaft- it will tighten up as you raise it. It may be at this point that you determine that it is too tight, and needs trimming. If it doesn't tighten up to the point of binding, then you should be good to go. You don't want to cut the shaft if you don't need to.
I can't imagine the dealer delivering it with the shaft too long- I think it is more likely that you haven't learned the trick yet. If they did deliver it with the shaft too tight, then let them trim it- it is their responsibility. Let them assume the risk of cutting the shaft too short, and having to replace it.