I have heard it depends on the dealer...once you dump the exhaust they know you probably added a tuner and if they want to bust chops they will.
It does depend on the dealer (which is illegal).....but they claim it's the MoCo. The Magnussen Moss Warranty Act basically says that the failure has to be directly related to the failure for them to be able to deny the warranty.
All of my bikes since my 89 Ultra Classic have been modified but it's never become an issue with the factory warranty or the extended warranty (service agreement). Most recently, just a few weeks ago my wife's bike (09 Street Glide, cams, tuner, exhaust and Ness Big Sucker air cleaner) started making a noise in the primary and we took it in. The run out was .0015. In two weeks they had received the new motor made with her VIN stamped in it, from the MoCo and had it back in the bike. We also had the chrome inner primary installed since the labor was free. Mods were not an issue.
My bike, a 10 SESG (cams, TTS tuner, Fullsac baffles, dyno tuned,etc), took it in last week for...........you guessed it..........noise in the primary. My noise was different than my wife's and could barely detect the noise but I didn't wait.......got it in there. Mine turned out to be the compesator. They replaced the compesator, spring assembly, etc. and I should get my bike back when they open on Tue. (closed today and tomorrow). The mods have not been an issue. I've never heard of mods being an issue at any of the dealerships here in Calif. unless they've been mods that are over the top (ie. 11:1, etc.) but certainly not with what I consider street ridable mods.