Nothing you do that doesn't land you with an R title will void the entire warranty. But some things you do might void certain parts of it, and it is totally at the discretion of the dealer doing the work.
There is a list of certain performance parts in the clean air act that can't be used to void a warranty claim, and the simple presence of aftermarket parts cannot legally be used to void the entire warranty. But if the dealer thinks that some sort of aftermarket modification caused the failure of an original part by placing it under undue stress they can refuse to warranty it (although most won't because they don't want the headache). Also, modifications that replace factory parts will obviously Ford won't cover someone else's part. For example, if you put a suspension lift, and leveling kit on it, and some 35 inch tires, and then the front wheel bearings and upper ball joints fail within the warranty period they are going to argue that the bigger tires and modified suspension geometry places the wheel bearings and ball joints under stresses that the factory configuration wouldn't have, and caused them to fail prematurely, and won't warranty it. IMO they would be correct and justified in doing so.
Or if you lift it 4 inches, and replace the factory shocks with some Bilsteins, and then one of those fail at 30K miles, obviously Ford is not going to buy you a Bilstein shock. You have to take that up with the people you bought them from.
What kind of stuff were you thinking about doing?