There really is not to explain. If truck come in exhibiting problems and lets say 'Headgaskets" are the cause. Ford warranty is going to pay the dealer to do the work. In order to do Headgaskets, the EGR system, intake, cab, bolts, etc etc, all have to be removed anyway, so if customer brings new parts, ie head studs, EGR Delete kit, etc... there is not any additional labor to put these parts on since Ford is paying the labor anyway. The only think I see extra here is the regulated return line. That would be a little extra work, but it depends on how much the dealer got paid. For example during my head work. Ford warranty paid upwards of 50 hours of labor for teardown, diagnosis, reassembly, and testing. The tech that worked on my truck was able to flag it in 30 hours, so he had a 20 extra hours he was getting paid for anyway. So if the tech that is working on your truck is cool, he'll toss in few freebies.
It all really depends on 2 main things. The Service Writer, and the tech working on your truck. If both of them are cool about the mods, then no problem, provided the dealer has a good history with Ford warranty(some dealers have a bad history and Ford will put them under a microscope for any large warranty repair.) But if the tech, and or service writer are not mod friendly, then no dice.