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.