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No one will have a concrete answer for you. You have to pay to play, you should assume if you blow a turbo they will deny the warranty, even though the freer flowing intercooler would be better for the turbo. Every dealer is different, some will flat out deny warranty on the spot and some are super cool and will try to warranty everything. Here's the rub though - if you have a super mod friendly dealer who is going to warranty a blown turbo for example, Ford Corp may get involved and want to send an 'engineer' to look at the truck. They could void the blown turbo warranty even if the dealer was willing to honor it. Obviously if your seat heater goes **** up they can't blame that on an intercooler.

I know this isn't the answer you're looking for but you won't find a definitive answer I'm afraid.