It is my understanding that mopar has a pyrometer that the dealer can install. The one I saw looked to be an AutoMeter UltraLight with a Mopar M silkscreened on the gauge face. Summit also sells the same Mopar gauge, as well as it's AutoMeter twin. I know that I read somewhere here that a dealer had installed one for someone.
My dealer has seen my 3 gauge cluster. They've never said anything but "hey that's cool, did we do that?" So far so good.
To me, gauges are a must. Before I had them, I didn't see the importance, but now, they are quite informative. You should be commended by the dealer for taking a measure of preventative maitenance like gauges. Anything to help you monitor/protect your truck should be smiled upon by the dealer. In my humble opinion anyway...
I would imagine that having a pre-turbo pyro probe could be an easy out for them if your turbo goes kaput though. An improper install could send shavings into your turbo thereby destroying it. However, a bad pyro install won't fill your crankcase with fuel (for example). Magnusson-Moss comes into play here a little. They would have to prove the gauges caused the failure.
My . 02 is find another dealer. One that recognizes the importance of engine monitoring.
As for the box/programmer detection. I dunno (some say yes, some say no). I'm not going to run one till my warranty is out or the truck is paid for (whichever comes first).