Along with the obvious sound difference I think it will be smoking like a 6.0 and they will know why.
Exhaust alone should not damage anything because the computer is still in control of the fuel and the boost based on IAT, ECT, Boost, and maybe some other things that would cause it to decrease fuel or boost. If you modify the programming the gutted exhaust should actually save the motor to some point because it should lower the EGT. The question is can they tell if the programming were modified as they have claimed.
In a warranty dispute they would have to prove that the unrestrictive exhaust caused some damage. It seems unlikely they would have any problem at all with a modified exhaust other than emissions problems. If your vehicle fails an emissions test and you loose the registration you would need to replace the parts where a delete pipe could have been easily reversed.
The exhaust modification warning is in reference to damaging the DPF. If it's not there then there is nothing to damage.
The real killer is the reprogramming warning. They would likely refuse any warranty claim on an engine failure if they could tell reprogramming had been done or if they had a way to tell a fooler was used.