The Ford franchise agreement does not include anything related to a dealership "performance division" or agreement that the dealer can install aftermarket components. The dealers that advertise these rogue "performance shops" often come up with convincing names like "Galpin Auto Sports" (GAS) or "Ken Grody Customs". It's all a facade to sell customers aftermarket parts with a mark up under the premise that they won't void the factory or extended Ford warranty, which simply isn't true.
Any aftermarket component, regardless of brand or who installs it, has the potential to void the warranty on any factory system if the modification is related or attributable to the failure that has occurred. So if the dealer installs a supercharger system and a piston melts down, that is between the customer and the dealership. It's not warrantable through your factory powertrain coverage. If the customer does not have a dealer-backed express warranty for the coverage of the powertrain should a failure occur due to the modifications, good luck.
FordTechOne is 100% correct regarding the warranty- Ford Motor Co will not cover any aftermarket modifications or replacement parts under warranty. It does not matter what your dealership tells you, unless your dealer is planning on covering the repairs on their dime. If they plan on running it through Fords warranty program it will most likely be flagged at some point through the warranty claim process.
I have worked at Galpin Auto Sports for the last eight years. We never tell our customers their upgrades or modifications are covered under their Ford factory warranty, their ESP (extended service plan) or third party warranty. We do our best to educate our customers and inform them of how this process works. I agree there is a ton of misinformation out there regarding modifications and what it does to the vehicle warranty, however I can tell you that our team at GAS in no way lies to our customers and tells them that their aftermarket upgrades are covered under their factory warranty. We pride ourselves in selling and installing high quality parts and services to our customers. Are we the cheapest shop in the city? No, but we strive to provide the best product knowledge in our sales department coupled with highly trained technicians who can install a wide variety of parts and modifications correctly and safely.
Lets say a customer purchases a Roush Power Pack from us and has us do the install. We inform them that their factory warranty will not cover the intake, tune (engine), exhaust and any potential issues that may arise from the use of these items. Now, Roush offers a 3 year / 36,000 mile warranty on their power packs. If something were to go wrong we would reach out to Roush and they would step in a take care of the repairs if it were caused by their product.
We also sell and install Ford performance items, which they offer a warranty for. We had an instance here where we installed a power pack on an eco-boost mustang and within a few thousand miles there was a catastrophic failure in the engine. I contacted my ford performance rep, they asked me to pull the ECU and over night it to them. Once they were able to confirm that it was their tune in the vehicle at the time of the failure they covered every penny of the repairs and the customers rental vehicle as well.
Two years ago we installed a Whipple supercharger on a 2018 Mustang GT- the customer called in a few months later saying the vehicle died on him while he was pushing it very hard, we towed it in and did a full diagnostic. Spoke with the team at Whipple and determined that yes the vehicle was being driven hard but that is what they are built to do and there was indeed a failure. Within 2 days I had approval to change out the short block on the vehicle from Whipple. Whipple covered the cost of the engine and we covered the labor to swap everything over.
My whole point in this long winded response is that we do our best to fully inform our customers of the risks and consequences of modifying their vehicles as well as benefits. We also strive to recommend products made by companies who will stand by and support the customer if something were to go wrong. We take time to test products or items before we recommend them to ensure optimal compatibility, performance, and longevity.