Calories? So what?

I keep seeing things about calorie content of foods in articles about healthy eating. I recently found a new breakfaast cereal -designed by CSIRO - which is supposed to be particularly good for morning nutrition. My wife's comment was - "not exactly low-calorie".
So what? Calories are not the only important factor; something that Weight Watchers seems to have taken into account with their latest alterations to the 'points system'.
But more than that, I am having a hard time understanding exactly how calories matter at all.
I am willing to accept that they do. Very many intelligent people have done very many studies about weight loss over many years. While the details keep changing (as of course they do in any real science) the general acceptance that energy content is an important factor is overwhelming.
The trouble is that the science has been simplified to the extent that the link is not clear.
If I knew less about science itself I could probably accept that 'energy' is 'burnt' is doing exercise and hence their is weight loss. Or that energy in food is stored as fat and hence less calories means less adipose tissue.
But energy can't be burnt! It is not a substance, it is not material (Einstein notwithstanding). And even if it could be, conservation of mass means that the residue - the 'ash' if you will - MUST weigh the same as the original material. The important point, which keeps getting lost in the reduction from scientific to popular language, is how the different materials are handled by the body. Chemicals (such as carbohydrates) which contain usable energy are stored by the body. Chemicals that cannot be readily used as fuel (or building blocks) are evacuated from the body. This may be as gas, through breath, as liquid, through urine or sweat, or as solid, as faeces.
This I can understand.
But it changes the way you think about foods and weight management. The equation is NOT 'body weight' = 'calories in' - 'calories out'. Despite being the message passed on by a hundred different weight management experts, that equation is absurd from a physics point of view.
Correctly it should be 'body weight' = 'mass in' - 'mass out'. However this carries the rider that the physiological response is different depending on the content of that mass. Which means that the amount of 'mass out' depends on the detailed composition of the 'mass in'.
The simplification is that the major factor is the calorific content of the food. But this ignores a great many other factors which are at play. The health of the body under discussion will affect its metabolism and reaction to food. The health is, in turn, impacted by the lesser contents of the food and by other elements such as muscular activity (exercise).
We can also see that aspects such as sweating can have a significant impact on immediate body weight; water is quite heavy. However, the major component of sweat is water which will be replaced very quickly and hence it is not significant factor is long term or durable weight changes. And, of course, water is enormously important in the correct operation of a body's metabolism so the short term loss can lead to long term difficulties in weight control. [In other words - always stay properly hydrated].
Of course the physiological reaction to food is SO complex and so involved that it is very difficult to explain. Especially to those who do not have experience in that type of thinking. Hence we have two or three pieces of advice relating to weight control: "Calories in - Calories out", the need for an exercise program for a health, what constitutes a healthy diet etc. And there has been natural confusion and misinterpretation because of they are not truly separate pieces of advice.
All these are different aspects of the same approach to healthy living. Doing one without the others leads to an unbalanced and therefore unsustainable lifestyle. [I am not advocating that you cannot *start* a life change with only one factor, only that all related aspects need to be considered if you want a healthy end result].
For instance, there are a great many messages about how many calories are burnt per minute of various exercises. Again - so what. Apart from the fact that it depends on so many individual variations (such as the existing fitness of the exerciser), the loss of calories *during* exercise is a minor factor. More important is the physiological and metabolic changes that the muscular action causes in the body. Your body is operating a higher level for hours (or even days depending on the type and intensity of the exercise) after you finish. An exercised body stores more energy in the form of intra-muscular glucose rather than as glyerides and cholesterol in fat cells. It is preparing for the next bout of exercise and will hold this state for some time.
The energy content of food is itself only one aspect. The other nutrients are very necessary to the smooth operation of the body and without them, the carbohydrates and fats are not processed efficiently. Hence a nutrious diet, even if high in calories, will lead to less problems with weight than eating only low nutrient foods.
In short, the energy content of the fuel is only one aspect in determining milage. How the vehicle is handled, how well it is maintained and the terrain it travels over are at least as important.

And that doesn't even consider the psychological aspects.