Dave, it's definitely time for you to find a new dealer!
When I took mine in for a warped rotor, the first comment from the service manager was that it was probably not covered by warranty, that it was likely caused by abusing the brakes, to which I emphatically said B.S. They called Kawi, and it was covered, no questions asked.
As for the TPMS, I would also contact another dealer. I agree it's unlikely the Dyna Beads would make it stop working, but all the same, I would find some way to remove them before taking it in. The TPM Sensors are covered by the warranty if they fail due to a dead battery. If the dealer will not help you, call Kawasaki directly, or go to another dealer.
I live in an area with one (1) dealer. Alternatives are an hour away. Over the years, partially because of the mixed results from the dealer, I have developed a very good relationship with a private bike tech, who actually does a fair amount of contract work for dealers. The guy is honest, fairly careful, and does what you ask. I would not ask him to diagnose the electrical systems, but most everything else he is spot on. At some point it is less about the money and more about getting it done right the first time. If you are in central Ohio and need a good bike tech, I'll be glad to provide the contact info.
Meanwhile, I continue to have a slow burn about having to spend that amount of time and money on a bike with 13K.
Ride safe...
Dave