Calorie is not a Calorie?

I thought this was an interesting article on calories. http://blogs.scientificamerican.com/guest-blog/2012/08/27/the-hidden-truths-about-calories/

I don't totally understand what it all means. It also seems like we usually OVERESTIMATE calories which is not really a big problem in the great scheme of things. Considering so many Americans are overweight anyway if they WERE trying to calculate calories isn't it better to overestimate. 

I don't know.

Thoughts?