Actually FORD Cannot. Void your warranty unless they can prove that something, You(customer) did damaged a part that is covered by warranty in other words if I blow a piston I'm screwed!! Because of all the engine mods but if My alternator goes bad as it did in the past they have to warranty it! Like they did , long story short a supercharger has no effect on your AC system !! And much less does it explain a incorrect diagnosis just to charge you more for something they did not do yet you(customer) are still paying for , last time I when I had my timing gear problem they made me pay another 110$ for a diagnosis that said that my tuner! Messed up turned out that the pin on my timing gear was so weak that an incorrect shift caused the pin almost break in half. Bottom line something has to be done about these corporate thieves. The explanation I got was labor is 100$ a hour I was being charged 500$. So when I asked to get a breakdown adding freon takes 1.4 hours that roughly an hour and 25 minutes TO ADD FREON!!! It took me literally 5 minutes and then what. 3 and a half hours to put a relay and 2 fuses? Or like they call it "CIRCUIT BREAKERS" .. I will so all I can to get some closure I'm not Ms. Jackson that goes to get her oil done and to find out why she has no washer fluid I'm a mechanically inclined person and I know when I'm being screw.
Sure, they can't void it but they can run you in circles until you give up or pay up for a lawyer. There have been endless threads on warranty issues with modded cars. It's not worth it so don't tune or mess around with the engine until you warranty is expired. Simple as that