Just like said above...We use factory Mopar TB's, so from the outside, the dealer would have no idea that yours was ported. They would have to remove yours and hold it side by side with a stock TB to notice any difference.
As for the intake, they would have to prove that your intake caused a problem in order to void the warranty. If you hve the S&B scoop installed and you take the truck in for having a hydrolocked motor, then they are obviously going to blame the intake, but transmission or diff problems, they cant come at you saying that the intake is giving you so much extra power that it destroyed your transmission.
On top of all this, they can only void your warranty on the part that was swapped out. The rest of your warranty will remain in tact on any parts that are not aftermarket.