My own experience so far with my 6. 7 says the dealer has no idea how the new emissions work. When I brought my truck in for the particulate filter being full, they determined the #1 egt sensor was out of range and need to be R&Red. Since they needed to order it, they said to keep driving the truck. I told them that was stupid, and it could ruin the particulate filter. I didn't drive the truck until I had to drive it 1/2 an hour back to the dealer when they got the sensor. It barely made it, and stalled in their lot. They replaced the sensor, and then tried to drive it! It died completely 2 miles from the dealership, and they had to remove the exhaust at the downpipe to get it back. Then they had to order a particulate filter. The particulate filter can be plugged bad enough that it cannot be regenerated on the truck and must be replaced.
I don't think running these things with a bad sensor is generally a good idea. At best, the engine will determine something is wrong and go into limp mode. At worst, the engine won't know anything is wrong with the sensor and will be operating with false information that could break something.
If you are running with the latest version of SW, 3000 miles on a particulate filter is not encouraging. Especially given the fact you are working your truck they way it should like to be worked. As far as I have been told, "taking it easy" on these engines, especially idling, is the worst thing you can do to them.
For now I guess all we can do is follow the dealer's advice (informed or not) so they don't void our warranty