There is nothing wrong with turning up the truck. It belongs to you, you are accepting the risk of doing whatever you do to it. Do what you want, it's yours. 

Read the warranty.  I guarantee you that it is going to specifically state that the warranty is voided by making modifications to increase fuel delivery.  There is nothing unreasonable about that, and even if you thought there was, you had the choice to not buy it because you didn't like the warranty terms.   

Turbo failure not related to increased fuel delivery.....that's gonna be a pretty hard arguement to win I'm afraid.   How do you prove that it is not related, especially since overfueling is about the surest way to ruin a turbocharger?

The Ford dealer has a responsiblibly to his franchize to not submit false warranty claims.   If he was aware that the fuel system had been tampered with, he was obligated to state such on whatever forms were filed for the warranty claim.  He was clearly aware of it in this case because the rocket scientist son put it in his shop in a tampered condition.  I just don't see what there is to fuss about here, the parties have made it all very cut and dried.  

If you're going to cheat the warranty, do it on your own, don't put the dealer in a position where you expect him to lie for you.  He's an idiot if he does that.  If you protect him from knowledge of the tampering, then he isn't put in such a position, but someone up the chain is still likely to be suspicious of overfuelling when a turbo is melted down. 

Once again the theme is you take your chances and you pay your costs.