i just had it in this weekend, i restored the original backup first, then brought it in. i am not sure if they did diagnostics, but they did say they were having an svt inspector come out to check for chip/pulley. my car was in to get the rear differential leak fixed. they didn't say a word about my mods, and said that intake and exhaust are fine.
I have, left the pulley tune on and put the pulley cover back on to cover my after market pulley. Dealership said nothing. I have been going to regular service and warranty issues for some time now with the 3.2 pulley installed, just install the pulley cover. The same dealer replaced the tranny in my 01 lightning with a chip and pulley that was easy to see. So I guess the moral is it all depends on the dealer.