Actually I would imagine that if an owner kept up with those updates before the 3/36 and/or 5 year power train, new updates would not be an issue
Mine the last it was in had no new updates available. Mine, a '14, I believe has a 5/100 power train.
Now there are updates and there are updates. There are required updates but there were some the dealer did not do as they were to correct an existing issues only.
The dealer only does required ones. I have only had 1 TCM/PCM update other than the recent cable one. Many TCM updates have been issued but only one was required for my Cherokee.
My transmission is very smooth though at half the mileage of @Dodgeboy
Now the one point I would make is I really believe that FCA is responsible for updates issued after the warranty expires if applicable to your vehicle year and VIN.
As the OP mentioned there are charges after the warranty period. But in his defense I would say that transmission should be smooth, at this point in time, and not require any further updates to make it so.
Any issues with shifting if recently developed, is not a good sign for the ZF. Especially true if its the old hardware equipped transmission. All my dealer told me on my '14 was if I ever notice a change in transmission behavior to get it in to them.
Also by the way I do hope that the dealer took care of that shifting issue for you with that update. You are definitely one of the long term testers on this forum so I can get a view of my future with my Cherokee.