Excellent question. Here's an indirect answer. We humans have an old saying: Seeing is believing.
Doggies have a different saying: Smelling is believing. A large proportion of a dog's brain is devoted to processing various odors.
Your JR is scent-marking the puppy, as a message to other dogs: This puppy is part of MY wolf pack. Oddly enough, this strange behavior is really about affection.
If an adult human did the same thing to a human child, the meaning would be entirely different! Sometimes we inappropriately anthropomorphize canine conduct. That said, if this behavior is happening indoors, it would be a good idea to reinforce basic house training.