in my experience as a Ford tech for 17 years
all the modified vehicles like Rousch,Saleen and even the Ford SVT need to have warranty work done by certified techs for those products.
the dealer i worked at did do some mods to diesel trucks,but like mentioned it was all suspension,tires wheels etc.nothing to the engines or drive trains.
once you start modifying the power train you void warranty unless its an approved mod done by an approved mod company(i,e, rousch,saleen etc.) and then again they are only warranteed by the approved dealers/techs/companies.