I know someone who bought a truck with tuner installed by the dealer. The warranty is by the dealer and not FMC. This was acknowledged up front.
I believe the warranty issue is BS anyway. Leave it stock or be prepared to pay, period.
The truck is setup for the acceptable risk factor of failure. Exceed that and it's yours.
Nobody installs a chip because they want to feel better about it. It is for more power. If you want to remove the DPF that's your baby. It is illegal or they would not put it on there to start with. Your economy is not going to improve without removing the DPF. You will spend the money saved on fuel to replace or clean the DPF.
Basically leave it stock or forget the warranty. If a repair is covered that's great.
People have been towing and will continue to tow with less power than the stock truck has. You can tow with the truck as it comes from the factory without any problem.