Anytime you modify, you risk having problems with your warranty...period. Many people will tell you that according to Magnuson Moss you can mod to your hearts content. Technically they are right, but it doesn't mean the dealer has to make your life easy about it. Also, if you find a dealer that doesn't give you grief, are you confident you will always have access to that dealer (never move, guarantee new ownership won't change the rules, etc).
The most extreme I've seen of this is a Challenger buddy has a supercharger and mods galore. He recently went to the dealership (very good relationship) and they will still honor factory part warranties. It surprised the hell out of him, and I think everyone else too. While guys like this exist, I prefer to think they are the exception vs norm to the rule.
My point being -- modifying can cause you warranty issues. If you aren't comfortable with those risks, then don't take them.