You probably won't see much of a gain with a throttle body unless you have some kind of power adder and are making lots of power. I know we've made almost 800 RWHP with a stock TB on a '05. Both the TB and Pulleys are fairly easy to remove, so if you did for some reason have to take the car in and were worried about those items, you could remove them and re-install the factory parts. Personally, I wouldn't worry about it. I've had several modded Mustangs serviced under warranty and never had any issues, but I guess it could depend on the dealer.
I know Ford and GM differ, but I even had a clutch warrantied in a head/cam Corvette and it was obvious it was modified by the lopey idle and loud exhaust with LT Headers and no cats.
As red05bullitgt said, unless it's proven the actual aftermarket part was directly responsible for the warrated part or parts to fail they have to cover it.
I just noticed your first post says it's dyno tuned, so technically it is "chipped."
-Rick