first of all, legally, they canot void your warranty. secondly if somehting goes wrong and you need warranty work it has to be proven that what you did, mod, was the thing that caused the problem.
for example if your engine motor mount breaks, hey cant just say your warranty is voided due to you leveling your truck.. it has to be proven that the level kit broke the mount. this statement is just for example sake.
You have brought up a good question though, as i am wondering if by lowering the back end of the truck if that is going to throw the front end out of alingment or put a different angle on the ball joints. sounds crazy but if you dont know you just dont know.