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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.
Yeah it definitely isn’t the whole story. And protein is a great example. It takes about 15% of the calories in proteins just to break down the protein, so you sort of get that as a discount. But that can be said as calories out immediately goes up by that 15%. :)
To add further nuance to what you've said, (I know you know this already, so this is for other readers) when we ingest sucrose it is converted into glucose and fructose, which causes our blood glucose to rise steeply, which then results in a commensurate steep rise in insulin secretion. Elevated insulin causes many cells in the body to uptake glucose and chronically elevating insulin from a constant intake of carbohydrates means that the adipose tissue have no choice but to keep converting glucose to fat.
Sufficient ingestion of protein too will cause an increase in blood glucose levels, but nowhere near as steep nor as high. The biological effects are entirely different. And for anyone curious, it's possible to visualise this by wearing a continuous glucose monitor. It'll provide a lot of insight into an aspect of how eating different foods can affect your body differently.