That was a very interesting article! (I hope I'm allowed to post even though this is kind of old. ) I noticed this a long time ago, and with other people's dogs. I work with the trainers at the local shelter a lot and people would come up and say "I exercised him so much, why is he still crazy?"
With Dakota and Alice (More so Dakota, Alice is at the beginning stages.) I have them work for their reward (Throwing the ball, tug, flirt pole, etc) and during play. I'll throw the ball for Dakota and say "Platz!" in the middle on his chase, he downs, "Yes!" he gets the ball and comes back doing his funny happy run that he always does when he does something right. I'll make him heel for a tug, I used his tug to teach him to out on his tug.
I noticed, even in doing a lot of stuff like that I was lacking eye contact/focus. So I started having him give me eye contact for almost everything. When waiting for food in the morning, before I throw the frisbee, before I tug.
When we bike, I have different commands for speed up, slow down, left, right, move over, and when we stop to cross a road I taught him to automatically go to my side and sit until I say "okay" and we move forward.
And I have to say, when they said "Dogs are born to save energy" I couldn't help but think "Have you met a working Malinois?"