Basically, if you have engine trouble, they will likely try to blame it on your mods. Now I have heard of "mod friendly" dealerships who understand the aftermarket and are rather accommodating. Also, you don't void your warranty. You just run the risk of a claim being denied if you have a problem like a spun bearing etc. Now if a shock blows out, different story. Anyway, you get the idea.
The more you hang around here, the more you'll the same question asked....I promise. It comes up by-daily. You'll eventually get the full low down. I'm just too lazy to go into any more details or hypotheticals lol.