Well... Speaking from experience... dealers Have no problems with mods until they cause a problem. They try to blame the mod as soon as something goes wrong.
MINI - Had a Highly modified MINI and the dealer gave me crap about a couple standard repaird and i was able to argue my way around it. Even though a significant portion of modifications were installed by the dealers.
Subaru - I only had a Tune. Period. Blew after 3,000 miles... they Did not cover it under waranty (pulled some Goodwill "go F yourself next time" dodo) even though they told me at the time of purchase that i could go as far as stage two w/ no probs...
Short story long... When (not if
) you modify your car and IF (not when) something goes wrong during the waranty, expect a Hastle. If you Race, expect a Hastle.
If your willing to deal with the hastle... mod away... if not... think twice.
One of the biggest problems is that when they put a couple turbos on... you can tune the crap out of them and get a ton of power relatively speaking, and things break. They are protecting themselves. :shrug: MINI (aka) BMW has been relatively fair. Subu not so much.