More on energy balance

After the last post it occurred to me to wonder how the energy content on food is calculated. I can measure the weight easily but how do I know the energy that I am consuming. The major method is to read the label on the packet. This is not very useful for fresh foods, but there are (apparently) on-line sources that can provide the information.
But this only shifts the explanation back a step. Tracking back, further the best explanation I can find is from Scientific American which states:

The original method used to determine the number of kcals in a given food directly measured the energy it produced.The food was placed in a sealed container surrounded by water--an apparatus known as a bomb calorimeter. The food was completely burned and the resulting rise in water temperature was measured. This method is not frequently used today.

And

According to the National Data Lab (NDL), most of the calorie values in the USDA and industry food tables are based on an indirect calorie estimation made using the so-called Atwater system. In this system, calories are not determined directly by burning the foods. Instead, the total caloric value is calculated by adding up the calories provided by the energy-containing nutrients: protein, carbohydrate, fat and alcohol. Because carbohydrates contain some fiber that is not digested and utilized by the body, the fiber component is usually subtracted from the total carbohydrate before calculating the calories.

Which answers another question I had about calories which cannot be absorbed by the body and therefore pass straight through - e.g. fibre. As usual Wikipedia also has a good description.

And this is the simple part of the Energy Balance equation. The link between burning energy and losing weight is still opaque.
Which I suppose is the problem. This explanation is superficially simple, but once the surface is scratched there is a great deal of complexity involved. I don't mean just in the biochemical and physiological reactions taking place - that is expected - but in the actual correlation between energy balance and weight control.
So why is it so widely used when a mass balance would be so much simpler - to apply as well as to explain.

Thinking about it, the mass balance view is purely and simply descriptive. It is self evidentally true but provides no further insights since the "mass out" end is so tightly dependent on the composition of the "mass in" end. And once you get into composition, we start talking about energy content.
On the other hand the energy balance view attempts to provide a simplistic explanation as well as a description. It states a casual association - a body attempts to hold onto excess energy and therefore stores it, generally as fat. In other words - weight gain is caused by ingestion of too many calories. It skips over the source of the fat molecules and the elimination of metobolic by-products, as being a trivial aspect.

But I still think there is some benefit in considering the impacts of this "trivial aspect" of the whole process.