Of my two local dealers, one is my favorite, because they treat people right. I didn't buy my bike there, because they couldn't get one from another dealer, but one of the salesmen used the bike locator and found me seven (7) 2011 CVO's scattered throughout the mid-West, one of which I bought. He didn't make any $$'s on that, but he knows he has my business for parts, clothes, and any service that I can't/don't do myself on previous bikes and this one. When I had 300 miles on the bike and was complaining about the cat heat, one of the other salesmen was trying to talk me into a full V&H system, because thats what their in house dyno man likes the best. I told him I had already ordered my Fullsac Stage 1, he had never heard of them. The Fullsac stuff arrived mid-week, with a T-shirt, which I wore to work the next day. I rode by the dealership with a question for the service manager. He saw my Fullsac shirt, and said "really good stuff!". I replied, "yeah, it came yesterday, I'm putting it on this weekend." They put exhaust and maps on brand new bikes before they ever leave the floor. Once you get it broke in, you take it back for the dyno sessions, if needed/wanted. I'm sure if you have a warranty issue, they can determine if the aftermarket/modified part caused the failure or not, and react accordingly, without using the modified part as an excuse to not do the warranty work.
On the other hand, I went by the same dealer today, and a new salesman told me I shouldn't make any mods until the warranty had expired. It all depends on who you talk to, and how much they know about the Magnuson-Moss Warranty Act.