Your warranty rights vary state by state. In most cases it boils down to the parts directly affected by the modification.
If you do a suspension lift and wider rims with large tires and a wheel bearing or tie rod fails, its on you, the same can be said of a trans failure due the the increased gear ratio. Brakes will also be affected by stance and tire size. But things like interior electrical and engine would most likely not be affected. They do have the right to charge you for any added labor that may be required to do a repair due the added height or any add on components that may be in the way or those that take longer to remove and reinstall.
In many dealers, the guys that can decline a repair often never see the truck, the job ticket gets written up and only the technician sees the truck. It's often up to the tech whether he complains that it's caused by an aftermarket mod or not. Usually if he doesn't feel that it's a problem or if the normal repair isn't causing him any added grief, most wont bother to say anything about it.
I know from my years in a dealer shop that if a truck came in lifted to the sky and covered in mud and it meant that I was going to have to climb, crawl and get covered in mud to fix something that would normally be a quick fix on a stock truck the customer didn't have a chance. If an owner took the time to make sure it was clean and ready to be worked on, I ussually wouldn't bother worrying whether or not the warranty may be voided.
Keep in mind that the tech at the dealer gets paid flat rate, in other words, every job has a fixed price and set amount of time that he gets paid, if a particular modification makes the job take longer, the tech makes less money. There's no one out there that wants to work for free, so at that point the tech will usually get a manager or Ford rep. involved. The result will either be added time to do the job, or Ford may decline to cover the repair at all if the manager feels its up to Ford and gets a rep, involved. It often depends on who looks at it, what is wrong and what mods have been done.
I would say that 90% of the time if the truck is clean and well kept and the mods are well done and complete, they will warranty it with no trouble.
You may want to talk to the dealer that would be handling any warranty, see how they handle such situations. It doesn't hurt to ask. If you don't get the response you want, try another dealer, maybe one that sells more trucks than cars. The dealer is not the one to determine whether or not an item is warranty, it's up to Ford if a question arrises. If the dealer refuses a repair, you have the right to have Ford look at it. Often the dealer balks at doing a warranty repair if they feel that Ford may not pay the claim. There's an phone number in your owners manual for that too.