Third-party warranties aren't worth the paper they're written on. For engines, they typically only cover a very short list of "lubricated engine parts", and head gaskets aren't on that list. Every single one I've ever seen has exclusions that are at the discretion of the warranty company's rep, who must approve all claimed repairs prior to the warranty company agreeing to pay for them. The most common weasel-words for exclusions are "normal wear and tear" and "abuse". Since the warranty company doesn't make money if it pays a claim, it's in their best interest (and your worst interest) if they refuse coverage.
Chipping/programming a truck with an aftermarket unit will, 100 times out of 100, be classified as "abuse" by any third-party warranty company.
And also keep in mind that the vast majority of third-party warranty companies are "here today, gone tomorrow". They'll cash your check in a hurry, but good luck finding them when you need to make a claim. Those that are still around to answer the phone will delay and dilly-dally on sending an inspector to the shop, and won't show up until after you've already agreed to pay the shop for a teardown so they can inspect the parts before they declare it either "not a covered part", "normal wear and tear" or "abuse" and refuse your claim, leaving you with a dissassembled engine and no recourse but to pay the shop out of your pocket for the whole enchilada.
Do you get the idea I don't like these guys? Good. I don't. I have *never*, not ever, in many, many years of exposure to this racket, seen a third-party warranty company actually pay a claim.
But if you think you must, please check out the company with the BBB before you give them any money.
Keep in mind that the VIN from on the original poster's truck is likely flagged in OASIS for anything powertrain-related (engine, trans, transfer case, propshafts, axles) because of the aftermarket chip. This should not impact warranty on non-powertrain items -- power windows, radio, interior trim, paint, body, etc.
It's really very simple. The OEM warranties the truck in its OEM specification. Anything that you alter from OEM specification is no longer covered by the OEM warranty -- and why should it be? You've taken it away from OEM specification using parts and/or programming code that have not been tested, verified, and certified (with USEPA/CARB) by the OEM. Logically, it makes perfect sense that the OEM would not warrant, nor want to warrant, some third-party's device or calibration -- or the OEM components directly impacted by the device or calibration. In the case of an aftermarket chip or programmer, the entire powertrain -- engine to drive axles -- is directly impacted by the changes in calibration.
Thinking about pulling the wool over the OEM by removing the chip/programmer before attempting to make a warranty claim on the powertrain? It's called fraud, and it costs every single one of us who buy new vehicles. Why? Because the OEM has to cover its fraudulent losses, and they do that by increasing the sale price of their new vehicls. It's cheaper in the long run, for both the OEM and its customers, for the OEM to employ some full-time people whose sole job is to sniff out fraudulent claims and reject them.
And don't think this is unique to Ford. Every single OEM doing business in the US has similar policies that limit or totally remove their liability for aftermarket alterations to their products.
Bottom line: if you're gonna play, be prepared to pay when things go wrong. The aftermarket companies don't have the time or resources to do all the rigorous durability testing that the OEMs do and/or are required to do by law. Consider that just the EPA/CARB certification process, which includes extended durability & performance testing for the duration of the required emissions warranty for a powertrain/vehicle combination can cost in excess of $10 million, not counting the calibration time and labor that goes into it. Most aftermarket companies would be happy to gross that amount annually, nevermind spend it on one vehicle program. If you have a chip or a programmer, you are basically paying for a hack, a collection of tricks to alter inputs and outputs of the PCM.