I'm a student with Werner right now. My first trainer's truck did not have an APU. He idled it none stop the few weeks I was on there. His idle percentage was 75%. I personally saw that on the Qualcom. He stated he rarely ever turned his truck off in the two years he worked there. He also stated he was encouraged to idle less a few times but that was the extent of it.
My new trainer (10 times better BTW) has an APU and his truck does shut down after 3 minutes. Kind of annoying at times but it's the way it is.