I agree with much of what you're saying. Problems only arise when someone chooses to STRICTLY say calories in vs calories out is EVERYTHING or..that calories in vs calories out means nothing in the presence of manipulated hormones. Hormones undoubtedly play a role in how nutrients are used/stored. Again.. hormones are important. I think these concepts are much more clearly examined in the case of legitimate caloric defecit. Here's what I mean:
If I am in legitimate caloric deficit on a daily basis, I will lose body weight. This could be fat, muscle, water ..combination etc..but I will lose bodyweight. Now..the key here is, if I make sure my protein req is in place FIRST..then I adjust my energy macros around this set in stone protein req...as long as I stay in deficit, in the long run it will NOT matter. In other words.. As long as I make sure that my protein intake is first spot on..I could eat all fats for the remainder of my caloric intake (while staying in the deficit range) or all carbs or both..it would not mean shit in the long run. The only time it WILL mean something to restrict carbs when ALREADY in deficit is to manipulate water levels, or to reach levels of bodyfat % that a pro would reach on stage. Now..if you ONLY ate fats..or ONLY ate carbs as opposed to ONLY eating protein..well the same logic adds up..when the protein req are not accounted for properly..then things appear to happen much differently. Btw, if all those instances are in deficit, bodyweight will be lost over time..but they will probably look, feel and have health like shit.
In the case of surplus..macronutrients, IMO become much more important. Now that you are in surplus, your body is going to want to store nutrients...in this case hormone manipulation is more of an issue because weight is going to be put on..it's best to utilize your hormones in order to put quality weight on as opposed to just bodyfat. I have personally noticed little to no difference in regards to deficit and energy macros. As long as my caloric deficit is achieved and my protein requirements are accounted for..I have not noticed any difference in fatloss whether I ate the remainder as carbs, or as fats, or as both. In a surplus..I'm sure that if I ate all my energy macros (after protein is accounted for) by way of carbs all the time..things would be different because insulin will be ALLOWED to work its storage magic due to the surplus.