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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.