It shouldn't, but it depends on what fails and how the modification may have effected the failure. It may also depend on who looks at it.
Generally speaking any modifications from the cat back are fair game with both warranty and smog testing. The SVT exhaust will not be warranted as part of the car though.
There is never a clear cut answer with modifications but this one should be safe.
The Lincoln LS with a rod knock in our shop won't be able to be repaired under warranty though. It has a nitros system on it. A big no no.
