There not that naive, they can tell if you have modified the pcm, the key cycles just tell them to dig deeper. It is saved somehow beyond me.
I think you’re giving this too much thought & service techs/mgrs too much credit. I’ll be eating crow if I have a warranty claim denied down the road....but my experience having tuned multiple different vehicles via both handheld & custom dyno tunes I have never had a dealer bring it up during warranty-related service/repair on drivetrain. That includes a transmission issue on a G8 GT that was fixed under warranty even though they didn’t get it in until it had already eclipsed 100k Miles. I tuned it back to stock - that’s it.
It’s not like these cam phaser failures are a new/isolated phenomenon. I’m sure ford service departments get corporate bulletins/updates or whatever on common warranty repairs & Id wager the cam phaser issue is a commonly covered topic. So when a warranty repair becomes common across a number of different vehicles & the manufacturer is also aware customer satisfaction/awareness is now coming into play my guess is they’re more motivated to just placate the customer by running through the same motions they have in the past when a vehicle w/ the cam phaser issue passes through.
I have to imagine they’re more concerned w/ just identifying it, addressing ASAP, getting it back to the customer & moving on rather than wasting time digging for other possible culprits (like mods) for the problem when they’re fully aware it’s a common issue.
I will say this- have seen plenty of posts here & other f150 forums discussing/troubleshooting this problem- have yet to find any case of someone NOT having the work covered under warranty.