There is a type of seaweed that if your average American eats it, there are zero calories absorbed.
If most Japanese citizens eat it, they will absorb calories from it.
There is a gut bacteria common in the Japanese population that extracts calories from this type of seaweed.
"calories in" is that calories that went down your throat. It is calories that your body was able to digest, and "your body" includes many types of bacteria that are unique to each person and also unique to different population groups (meaning that some populations share commonalities in gut flora).
It is possible that certain antibiotics have wipe out some types of gut flora, allowing others to proliferate more. That alone could increase calorie absorption. (Or cause a host of other problems!)
It is possible that having a diet too heavily reliant upon one type of food results in an imbalance of some type. The problem is, this is a brand new area of research and we just don't know yet.
But it is sure as heck known that it is more complicated than "calories in food down the throat".