Perhaps their should very basic study on general health/weight of people who regularly consume refined sugars and those who abstain from refined sugar (with neither group engaging in structured exercise. Or have these scientists answer a more basic question about obesity...all things being equal, if you took a person (whether they exercise or not) would that person be more likely to be obese if they consumed a 200 calorie soda every day or replaced the soda with 200 calories of almonds. I think people would be greatly surprised to find out a calorie is not simply a calorie as is often suggested and that sugar has a lot more impact on obesity than fats.
I would be throughly shocked considering everything I have read is to the contrary. The much more likely issue is the soda drinker would feel compelled to eat/drink something sugary after a short period where as the person eating almonds would be satisfied. Interestingly you touch on this with your rat experiment and then somehow come to the conclusion "calorie is not a calorie".
In the end a calorie is a calorie in terms of the potential to expand your waistline, but a calorie is not a calorie in terms of putting the fork down and feeling satisfied. Maybe I misunderstood and that was your point.