Part of the problem with CICO is that we assume these factors are static within a system that is anything but. If, hypothetically, a material change in the microbiome prevented much of the calories in from being absorbed then those excess calories would instead be excreted. That would mean still mean the CICO model is technically true, but just not very useful as a predictive tool for weight loss in that case. Heart rate, metabolic rate, heat and many other factors might also play a role here, plus many others we don’t yet know about.
In most cases it probably is probably true that CICO is a useful guideline for weight-loss, but for those that say that it is all that matters, I think that is only true in a technical but trivial manner.