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You do not absorb all the calories. Those, therefore, are part of neither calories in nor out. I make no assumption here. BMR is a closely related topic but doesn’t change the calories in / calories out impact, which is what I am getting at and what most the remainder of your post says.
Nearly all of what you say here is correct and I wouldn’t dispute it. Except the last paragraph. It is, I’m sorry, categorically false. Calories in and out, in fact, simplifies nothing and does take things like brown fat and body maintenance prioritization into account; those simply change those two variables. I’m not saying the systems are simple. I’m saying the amount of carbon atoms absorbed into your body via energy stored in food and drink as one of a few macronutrients less the carbon atoms breathed out via respiration is a fairly accurate account of weight change. Everything else you’re saying is not in dispute. It isn’t easy and it isn’t simply, but calories in / out is not inaccurate, if still reductive.
I disagree, but I think we agree on a lot here.
Colorimetry measures calories in food by burning the food and measuring the amount of heat generated. This is different to what happens in cells for a huge number of reasons, so it isn't really reasonable to think of it as a good starting point for nutrition. If you take a substrate, say for example a fat, and you use it to make a hormone it is not being burned for energy and thus breaks the calorie in calorie out model. That is a simple way it fails.
I am not saying the disconnect is 100%, I am saying it is not 100% accurate and depending on how disregulated your system is it may be more or less accurate. Someone who is super healthy and of a low body fat percentage with a reasonable amount of muscle mass would probably end up fairly close to CICO for the first few weeks of a dietary change. This is not really in dispute.
The dispute comes from the rest of the population. We have more deranged systems which are less in line with CICO due to metabolic issues like insulin resistance, gut damage, gluten issues like celiac disease, and so on. The more deranged the body the more CICO loses its predictive value and becomes a bludgeon.
When I went to the doctor about my weight they told me to eat less and move more. My insulin resistance was not measured and the dietary recommendations led to more muscle loss and body fat gain. I had tonnes of issues with acne, dandruff, terrible body odor, mild scurvy, and overall ill health. Adding more food that I could actually digest and switching from my broken glucose metabolism to a ketogenic metabolism allowed me to repair damage, absorb vitamins more effectively, and fix all sorts of seemingly minor but overall stressful issues. My caloric intake was higher but I lost excess weight first by dropping glycogen and associated water but then by dropping fat while also gaining muscle. I felt like moving, I wanted to move, so I moved, but it wasn't willpower driving that like on CICO, it was hormones driving the change in output.
The calories being low led to conserving energy and being depressed and inactive. Adding good calories I could actually use led to more activity along with better mood and brain function. CICO is not a good model for making changes, it is just accounting. If you want to say "this many carbons came in, this many left" that is fine, but there is no why in that and no guidance on what to do from there. If you try changing how many calories go in or go out you shouldn't be surprised when the self regulating system regulates itself and changes something else, such as making you burn less energy or eat more food.
It is inaccurate, food manufacturers are allowed about 20% error margin when measuring calories. Calories have nothing to do with what our bodies do with the material we eat, since everything is a chemical process and we aren't closed systems. When we mobilize fat we create ketone bodies which are exhaled in our breathing, how do you propose to measure 'caloric expenditure' then? It is far too reductive.
Calories on a label are not the calories in the metabolic equation, so I don’t see how that is relevant here. Calories in are calories absorbed by the body, which is some subset of those taken in. Some come right back out the other side; we don’t count those. To say calories have nothing to do with it is bonkers to me. It is precisely the chemical process to which you refer. When we expend energy / heat / calories, we get that from food and drink. Yes, more immediate from one of the three major energy distribution mechanisms, but it all comes from what we put in. Then the carbon atoms stripped off of saccharides are bonded to oxygen and exhaled as CO2.
And all this to say, one cannot gain weight while eating fewer calories than being expended, reductive or not.
The calories on the label are what is used to make decisions when it comes to using CICO to decide what to eat, which is why it's relevant. I see now where you are coming from though, because I'm speaking from a pragmatic stand point, but yours is a theoretical one.
We do however appear to be in agreement, too. Due to these chemical processes CICO is highly reductive and pretty pointless for losing body fat, because what our bodies do in response say to 100 kcal of sucrose and 100 kcal of protein is entirely different, and result in entirely different biological outcomes.