There is often collateral damage from an implement PTO shaft that is too long and bottoms out. If the tractor's PTO shaft seal was damaged as a result of a too-long implement shaft, bearing damage could easily have happened as well. The bearing could have remained damaged but more or less intact until the seal was disturbed for replacement.
You know what you did wrong relative to the PTO shaft. You know that the seal was damaged. The shaft itself can't be shoved further inside the tractor without breaking something. You arranged for the dealer to repair the seal. If they hadn't "messed with the rear PTO" you would probably be here grousing about a repeat failure of the PTO shaft seal. Now you get to pay for the repair including the damaged part(s) that were discovered during the seal replacement. Call it tuition, and pay attention to the length of your implement's PTO shafts.
Yes, I know you don't like to read this. But it is true.