So many people site the
Magnuson-Moss Warranty Act whenever this question comes up, but think about this scenario...
what if you slap on an intake, and your transmission fails. The dealer might say, well, the transmission wasn't design to take on the extra horsepower from your aftermarket intake. They deny your warranty. Then what? You might be able to get Toyota to help you convince the dealership to help you, but what if they don't? You could take them to court, but who do you think will have the better lawyers? All the while, your car is sitting there with a broken transmission.
Long story short, anything you mod will risk part of your warranty going away. The dealership may play along and help you out, but there's always a possibility of getting screwed.