I'd agree with you for the most part - people suffering from obesity are almost never the people you'll see habitually snacking on lettuce and celery but quantity and quality of food are two different things. An average person could stuff away two large big mac meals with fries and a diet coke every day if we're talking purely in terms of calories (Morgan Spurlock be damned) so the nature of the food and how easily processed it is by the body matters a great deal.
However, speaking personally I've been keeping an insanely close eye on my weight and what I eat for the past couple of months and I've varied my diet an awful lot, just to see what would happen. Back when I was in the 14 1/2 stone range I was eating five pieces of fruit per day, two bowls of cereal with skimmed milk and an evening meal consisting of boiled vegetables and maybe some meat and I didn't lose an ounce (so I at least know my perfect diet once I hit my target size). Currently I eat probably twice the number of calories I used to in a given day but the weight is falling off me at a rate of about half a stone per month without any meaningful amount of exercise (I'm currently just over thirteen) I'm guessing that this is because I now have the energy to actually work off the remainder. Christmas gluttony saw me losing about a quarter stone and when I was off sick last week, doing nothing and eating pizza I lost another quarter.
Point is, eating the healthiest diet in the world won't lose you weight any more than the crappiest one will make you put it on so long as your calorie intake is at the appropriate level, which I guess is the point of this bit of research, some people will get the typical 500 calories from a big mac, some will get up to 1500 and since people trust calories as a scientific absolute, this is where a lot of the trouble comes from. That and body fat is a final last resort reserve for the body and it'll only dip into that once it has used everything in the cells, so someone with a more "efficient" digestive system is going to take an awful lot longer before their body needs the reserves.
Which is not to say that there aren't plenty of people out there who are "naturally" skinny or medium sized but are lardasses on the basis of an atrocious diet and lack of exercise but I don't think they're nearly as prevalent as society thinks. I'm not one for creating excuses for people who are eating themselves into a very early grave but I'm guessing that we're going to see a growing field of evidence that suggests that genetics are a large part of it. Junk food, in one form or another has existed for a longer time than this particular "epidemic" after all.