My dealer told me that it depends on the issue... IF the warranty issue/problem is directly related to the installation of the aftermarket piece, it would be void, or would fall on the supplier of that product. BUT, the dealer would have to prove that is was DIRECTLY related to that install..
In my case, If my tank failed, IF Ford would not stand by , Titan WOULD... I had several conversations with the owner of Titan during my buying process... Great guy ( forget his name ?? possibly Jim) , he actually also owns a few car dealers.. He gets in EARLY models and verifies the fit before they hit the market..