Why Does My Puppy Scratch His Bed?

It's been a week now since Charlie started this unusual behaviour that we find most comical to watch. We put an extra crate pad outside on the balcony to give Charlie yet another comfy spot to lie during rest sessions when playing in the backyard. Once he realized its presence, he began walking on top and scratching at it with both front feet at the same time. He was relentless at his scratching, increasing and decreasing his speed and never seeming to tire. 

After a handful of episodes, I started to worry that this was some form of repetitive behaviour perhaps indicative of something more serious so decided to see if I could find some answers.
The answers I found were nothing more than this behaviour was merely instinctual in nature. Dogs, originally of the wild, had developed this scratching behaviour to make a comfortable bed for themselves out of leaves, sticks and the ground and so over time this behaviour became an instinctual pattern. Other sources suggested that it was a territorial type marking again developed in the wild.

Sources suggested that if the behaviour was bothersome to families, pet owners could simply remind their dogs to stop the behaviour with their "no" command. I, on the other hand, see nothing wrong in allowing Charlie to be who he is and would never stop him from doing what he needs to do. If Charlie were to do the behaviour somewhere in the home where it were destructive, I would find ways to dissuade him from doing the behaviour in that location or providing other places that he could.