What scientists (and athletes) have known for some time now is that a calorie is not just a calorie, and a carbohydrate is not just a carbohydrate. The nature of the nutritional source matters, even if the end product of its metabolism is the same caloric energy equivalent. And the reason, quite simply, is because different nutrients are converted to energy through different metabolic pathways in the body. In the past, the importance of this fact was not well-appreciated; even though some researchers had sought to point this out, they were largely regarded as being on the fringe of mainstream nutritional science. Much has changed, however, with the elucidation of these specific pathways and the more recent revelation of the relationship between the human gastrointestinal system and the microbiome that it contains.
To address your specific points, the energy content of a "complex" carbohydrate (e.g., what we commonly think of as starches or long-chain polysaccharides) is extracted more slowly than a simple carbohydrate (e.g., what we think of as "sugars" which are generally mono- or disaccharides). Comparatively, insulin levels do not rise as quickly in the digestion of the former; there is more "processing" to be done by the body to break those long chains down and ultimately get to the glucose that cells then directly utilize to create ATP. So the first lesson is that anything that slows the rate of gastric emptying, or the rate at which blood glucose elevates after a meal, is going to have a beneficial effect on insulin regulation. The second thing to understand is that fructose is a pentose sugar that is exclusively metabolized via the liver, unlike glucose. Sucrose (table sugar) is composed of one glucose and one fructose molecule. High fructose corn syrup is essentially sucrose with a higher proportion of fructose, making it sweeter (as fructose is sweeter than glucose). Complex carbohydrates are not high in fructose. But we now have ample evidence that the consequence of long-term, excessive fructose consumption in a low-fiber diet causes liver damage in the form of hepatic steatosis and inflammation. The liver and pancreas work overtime and can't keep up. In fact, this is precisely what foie gras is: overfeeding geese with corn mash until their livers turn to fat, except in humans, this result is self-induced due to the neurochemical effects of sugar consumption.
Regarding endurance athletes, I would not say that they are necessarily healthier: they have optimized their bodies for physical exertion (higher VO2max, lower resting HR, greater muscular efficiency, higher lean muscle to fat ratio, etc), but this does not exactly translate to better overall health as measured by factors like total longevity and disability-free lifetime. In fact, we know that many of these athletes suffer from long-term health complications as a result of their training and competition, such as arthritic disease. In any case, if we are talking about how they are able to consume vast quantities of food yet remain lean, this is simply a matter of energy consumed versus energy expended. Yet the quality of the diet remains important even if there are no obvious signs of metabolic damage--sure, they might not get a fatty liver because gluconeogenesis kicks in, but even they know that they can't just drink 10 liters of soda to carb load.
The main driver of obesity in the United States is gross overconsumption of food relative to the energy needs of the average sedentary American. This is the imbalance in the basic caloric equation (energy in > energy out). And I say it is "gross" not in the "yuck" sense, but in the "it's REALLY WAY over the top" sense, because we're seeing people eat upwards of 3500-4000 calories per day when their expenditures are in the 2000 range. The secondary driver, which is what we might think of as "kicking the liver while it's down," is the extreme preponderance of calories from refined sugars, which do not trigger the satiety response as quickly as the equivalent energy content of dietary proteins and fats. Combined, this is literally a fatal one-two punch. Fat and salt may wreak havoc on the cardiovascular system, but refined sugar is like a drug: consumption creates cravings, triggers fatty liver disease (although not in everyone, for reasons still not entirely understood but believed to be related in part to gut microbiome) that is akin to the progression to cirrhosis in alcoholics, and results in Type 2 diabetes.
This post is already way too long but I have only scratched the surface of what is really going on in our bodies metabolically. The takeaway is (1) Stop eating well before you feel full, not when you feel full. (2) Eat more slowly. (3) Eat much, much more fiber. (4) Never drink sugary sodas or fruit juices; whole fruit is okay. (5) Choose fresh food whenever possible. Microwaving a pizza doesn't make it fresh. Note I say nothing about exercise, or fat consumption.