It really seems like they've switched cause and effect around, they eat a less energy dense/harder to absorb diet, and their intestines get longer to compensate, also they don't buff up as much, because they have to work harder for their nutrition.
Don't discount the role of genetics. Some people are just naturally larger, others couldn't get large even if they tried. Although Japanese people would no doubt be bigger if there was more of a weightlifting culture, they'd still be slimmer than the average American.
http://i.imgur.com/aHsayNH.png
From left to right, American, North Korean, South Korean.
A empirical illustration of both the role of genetic factors (American vs. South Korean) and the role of non-genetic factors (South Korean vs. North Korean)
It's a tiny sample of empirical evidence to be sure.
Simple as that.
Various groups of human populations will have varying sorts of phenotypes, depending on the original conditions of their population.
The 'long Japanese colon' may be related to the fact that Japanese are also better at digesting seaweed than other populations: http://www.wired.com/2010/04/sushi-guts/