“Calories in, calories out,” sometimes also expressed as “a calorie is a calorie,” is shorthand for the notion that calories are fungible; i.e., that weight change is independent of macronutrient composition. Another shorthand phrase is “eat less, move more.” You are right that the notion is false, but to say that “that’s not what CICO means” is also wrong, because the passages you quote are the very definition of CICO.
I suspect that you are confusing CICO, the ideology, with the notion of “energy balance.” Please bear in mind that nobody (or at least nobody sane) questions the thought that gaining weight involves taking in more food than we metabolise or excrete, and that losing weight involves taking in less food than we metabolise or excrete. And that is true, whether the weight gained or lost is lean tissue or fat.
The term CICO, by definition, stands for the hypothesis that increased weight is caused by one kind of energy imbalance, and decreased weight is caused by an imbalance in the opposite direction.
The hormonal-response hypothesis, on the other hand, reverses the direction of causality. The body’s hormonal milieu determines whether weight will be gained or lost by manipulating appetite to regulate intake versus expenditure. Furthermore, according to this hypothesis, the hormonal milieu also determines whether the weight gained or lost will be in the form of lean tissue or fat. (And we know from experience that it is possible to gain lean tissue while simultaneously losing fat.)
So in effect, we are all arguing the same thing, it’s just that you are claiming that the term CICO “means” something that the people who use the term never use it to mean. I agree with you that the term should mean what you say, but that is not how it is used in the scholarly debate. So when people on these forums use the term in the way you don’t think it should mean, they are just following the standard practice, not jumbled in their thinking.
To reform standard terminology is an overwhelming task. I don’t advise even trying. A wag once pointed out that “the Communist Party of the 20th century was no more communist than the Christian Church of the Middle Ages was Christian” (I’m a Christian, by the way, and I agree with that statement). But to try to come up with different terms from what those institutions called themselves is futile; they called themselves what they called themselves, and we just have to deal with it. And the same with CICO.