I'll agree with you that CICO doesn't account for a lot when it comes to meal timing and the various hormonal responses but I don't think it purports to. CICO is just a simple way of explaining the first law of thermodynamics and its role in maintaining, losing, or gaining weight. Different diets lead to different biochemical pathways for sure. But a healthy diet still must adhere to this law. It is certainly possible to have a bad diet and lose weight by only adhering to this one principle. This has been proven time and time again most notably by the nutrition professor who lost 27 lbs only eating Twinkies. I speculate that certain blood markers were a disaster. Alternatively, a person can fast and end it with excess calories of healthy nutritious foods and gain fat. CICO is not a diet, it is one law that healthy eaters should follow to meet their goals whether that be lose, gain, or maintain weight.
I wouldn't call food labels extremely inaccurate but they certainly aren't exact. They're still a good guideline though. Just like figuring what your Basal Metabolic Rate using the Katch-McArdle formula. It's a guideline, but it'll get you in the ballpark and you can adjust accordingly. Several months out of the year I do exactly what you referred to above. On Sunday I get the scale out and figure my meals and snacks for the week. I then eat the same breakfast, lunch, and dinner and snacks with the exact portions everyday. In a couple weeks based on the scale, measurements, and sometimes a DEXA scan, I'll adjust or maintain my caloric intake. It's not for everyone and maybe excessive but when I go back to my regular eating pattern I have a decent idea of the calories & macros I'm eating because for those several months I was weighing, portioning and counting everything that I stuffed down my gullet. All that said, you have some good points and it shouldn't be all about CICO.