So in essence, while the math might be mathin-and you look at it like “duh if you take X number of kcal out of diet, you will lose Y amount of weight/wk”, you will find that it doesn’t work up that way a lot of times for women.

There is a huge flaw in your reasoning. You're entire argument is based on the validity of a number that was spit out by an online calculator as a general estimation. It doesn't work out the way it's supposed to because you were plugging in the wrong numbers from the very beginning. Humans are heterogeneous. Estimations are sometimes way off.

All the little biological intricacies that you're describing are not proof that CICO is wrong. It's proof of how wrong the TDEE calculators can be for some people.

I have not used the app yet, but macro factor (made by Nuckols and Texlar from stronger by science) supposedly calculates your TDEE by tracking your caloric intake vs the fluctuations in your weight. In theory, this should be way more accurate.

CICO will absolutely work. You just may not like the numbers that you have to plug in.