At Philmont your pack must go under the dining fly at night.
Everywhere else, do what you want.
I put under my legs sometims if I only bring torso pad.
In sub 35 F weather I will have full length pad and may leave the pack outside or under tent vestibule, even if Im sleeping with the food. I do leave all pockets open so mices dont have to chew their way in to investigate. Ive hung it on the side of a tree or bush too just to make it harder for rodents if it doensnt look like rain.
I dont think there is any BSA procedure for what to do with packs at night, nor should there be any blanket policy.
If in bear country, your pack might have smells on it since food was in it, and it might be prudent to not have it with you. This topic can be debated endlessly, but remember generally bears dont want anything to do with people, they only want a free dinner.
However, considering that a bears nose is 7x greater than a bloodhounds, and a bloodhound can smell where a person walked 12 hrs ago, and what direction they were going. Bears have been known to smell dead carcasses miles away, even underwater.
If you had food in your pack, everything smells like it. Your tent, your sleeping bag, your clothes. Its just a matter of how much. IMO we are generally safe because bears DONT want anything to do with us, not because we have no residual odors on anything.