Your bodies absorbsion of nutrients and yes calories is not a system in a vacuum. Nor it’s decision to store excess calories as fat. There’s a wide range of how much different types of foods affect different people. I had a friend who would eat (we counted) 4000 calories a day and couldn’t get over 120lb. Turns out they had a soy allergy and their bodies didn’t absorb the food.
Simplifying it to calories in calories out is a generalism of a generalism.
So your friend was unable to digest at least a thousand calories a day, likely more, and didn’t see fit to mention the endless diarrhea they must have been experiencing? If you’re spewing a thousand undigested calories out of your ass every day, you should know something isn’t right.
Yes, nobody is disagreeing with physics. But a discussion about weight gain/loss that always has people saying "calories in = calories out" is like a discussion of every business saying "well profit = revenue - expenses". Obvious but not helpful. The interesting thing is discussing how to modify those variables.
The flipside of this is that people generally want to argue endlessly about what are essentially micro optimizations instead of addressing the core issue. Maybe your gut flora are “out of balance”. Maybe your metabolism is a little lower than average. Sure, there are factors that can matter. But if you’re not losing weight you’re not in a caloric deficit. If you’re not gaining weight, you’re not in a caloric surplus (or you’re spewing diarrhea and should talk to a doctor).
Address the core issue first before arguing about minutiae. The emphasis on relatively low impact factors is especially unhelpful and unhealthy because people latch onto all these discussions as justification for why they can’t lose weight. Sure, an obese person might have a low metabolism[1], but if they eat 3500 daily calories and live an entirely sedentary lifestyle, those are probably the major causes.
[1] But they don’t. Study after study have shown that obese individuals have high metabolism because metabolism is tightly correlated with total body mass.
Most people aren't fat because they're lazy. Most people are fat because they eat too much. We have a culture that glorifies food, junkfood more than the rest. Overeating when eating junkfood is absurdly easy. Teaching people how to eat healthier and eat less is the best known way to help people lose weight.
Constantly talking about genetic predispositions, obscure metabolism suppressing viruses or gut flora does about jack shit to help people lose weight.
The minor difference between the weekly calorie expenditure of the average person and the morbidly obese is mostly meaningless. It’s much more about how much they eat.
That’s because waste generally doesn’t contain any significant usable calories. If you’re passing undigested food then obviously it starts to matter, as abusers of laxatives know. It’s not typically discussed because it’s not typically a meaningful factor and if it is you should already know.
Yeah, crapping out calories is a time-honored tradition among people with eating disorders who don't like to vomit.
Your body doesn't care how the calories go out. If they're gone, they're gone. If you eat 3000, but crap out 2000, your body doesn't say "Yeah, well, that's not how you usually get rid of calories, so get fat."
Just because our methods of recording aren't perfect doesn't mean that the core idea is wrong.
Simplifying it to calories in calories out is a generalism of a generalism.