I love the MPT tune and honestly have a hard time driving the truck anymore with the stock tune. It makes a very noticeable improvement in performance. I personally felt that their transmission programming was too aggressive for me and held gears a little longer than desired, but many others seem to like it; it is nowhere near as aggressive as Sport mode, but you still maintain higher RPMs than needed for normal driving. I have the 93PRX and 91 Tow tunes with stock transmission tuning and also a 93PRX and 91 Tow with the stock transmission callibrations except it does not skip 2nd and 4th gears.
As for warranty issues, everything about the tune seems very natural and runs very smooth, so I have no worries. In addition, I did an extensive internet search and honestly couldn't find anybody else reporting damage due to an MPT tune, so it is probably pretty safe. I simply return my truck back to stock before taking it to the dealership and they have never said a word.