This is governed by the Magnuson - Moss Federal Warranty Act.
See
www.sema.org
Look under "Consumers" then click ON "Warranty".
Obviously a Dealer does not have to warranty a non OEM part or an OEM part that has been modified. However they can not blame the failure of an OEM part on another part be it OEM or aftermarket just because it is installed.
They would have to prove the shifter caused Tranny damage which would be difficult as our tranny has pattern failures with the Aluminum shifter forks, synchros and clutch failures as well.
The shifter and Tranny are 2 different parts/assemblies.
However, even though our tanny has internal STOPS, some installing the Hurst shifter are omitting the STOPS included with the shifter. The STOPS were engineered as an added safety feature to protect the Tranny and the Shifter. If you omit the shifter STOPS then you are opening the door for the Dealer to deny the Warranty on the Tranny AND the Manufacturer to deny a warranty on the shifter by using a part in a way not recommended by the manufacturer. In the medical field this would be classified as an error of omission and would be either willful negligence or malpractice.
If you use the Hurst shifter as indicated by the manufacturer and include the shifter STOPS then you are actually adding a safety feature to prevent damage to the tranny and the Dealer would be hard pressed to prove any damage by the shifter...in fact he couldn't. You are actually improving the factory engineering.
BTW the Hurst shifter is the only aftermarket with STOPS, as far as I know. I recommend it.
Still, if the Dealer is a real jerk, it is not a bad idea to reinstall OEM parts before taking it in for a Warranty repair.