it's pretty much up to the dealer and individual tech if they want to cause problems or not. i dont personally give anybody a hard time for aftermarket components unless they clearly damaged a ford part or are the actual problem. one example would be a lift installed by the customer in his driveway and now wants suspension noises covered under warranty.
some dealers will go out of the way to screw people though and unless you feel like going to court it's best to just find a better dealership.