But it takes a lot more than "the first few miles" for something like this to show up. This truck has not been off road yet and has less than 5000 miles. This should not be like this. I'm taking it in assuming it IS a warranty issue. We'll see what they have to say.
Only 2 possibilities are a defective brake pad (warrantable) or road debris getting between the brake pad and rotor (non-warrantable).
As far as machining the rotors, the OEM rotors have enough material that they can be cut a couple times before reaching minimum thickness.
When you bring up rotor machining, many folks think of having rotors cut on the old bench lathes and experiencing a brake judder/pulsation afterward. This is not because material was removed, this is because the rotors were machined to be true to the lathe, not to your wheel hub. This results in rotor runout, which over time turns into thickness variation, which is the pedal pulsation you feel.
The new on-car lathes from Hunter and ProCut machine they rotor while it’s still on the hub. This allows for a rotor to hub runout measurement that is better than when it you’d get when installing a new rotor. They’re auto adjusting, so there’s no technician error. It is a warranty requirement that every dealer have an automatic adjusting on-car lathe, so if they tell you they just use the old bench lathe, find another dealer.