My advice: Ask the service manager to drive with you. SHOW him the issue. Don't expect him to go find it. If the mgr says "they are all like this" ask to go drive a like unit. If you are unhappy with both, there is nothing to be done.
The transmission has engine braking in all gears but 1st. You may be feeling DFSO,(decel fuel shutoff). The injectors get turned off on decel to save fuel. When you put it in Neutral, the injectors need to light off or you will get a stall. So, when you go to N, you are actually re-lighting...
One of the guys I worked with got his 30 in and left. His last day in the office was 3/13 when they sent engineering home. It sucked for him, since he got to say goodbye to nobody. I hope things get back to normal before I retire. I would like to go have a beer with both of my friends.
The power on/power off modes and their relation to the shift points and braking rate are critical for coasting downshifts. You just changed them all. I'm surprised the dealer even covered it under warranty.
It is just better to not do back to back to back engagements/garage shifts without ever releasing the brake. The suspension can get loaded up and the results may not be as clean. The way you stated it should be fine.
You need to keep in mind that you have software reacting to what it sees...
General Adaptive procedure:
Heat the transmission to something over 70c.
Perform minimum throttle upshifts to at least 8th gear
Coast down with minimal braking
Perform N-D 8 times. Release brake between events
Perform N - R 8 times. Release brake between events.
TSBs are performed if the symptoms dictate it for a warranty return. The dealers generally don't just apply every TSB that is on a particular vehicle, if there are no symptoms.
If you are setting a wrench light, you should have a code. I would not attempt to clear it yourself, including disconnecting the battery. The stored codes should help the dealer with the diagnostics and you don't want to lose that.