the laws of physics apply to everything. everything we understand about biology can be explained by chemistry. everything we understand about chemistry can be explained by physics. it is the foundational scientific discipline.
i don’t have time to fully educate you about what a “closed system” is, but it’s a fundamental law of the universe that energy can be neither created nor destroyed, only converted to another form. when you sum all of the energy entering a closed system (such as the human body), that’s energy “in”. when you sum all of the energy leaving a closed system, that’s the energy “out”. if these two amounts are not equal, then you have either an energy surplus or an energy deficit. in the case of a surplus, that extra energy is converted and stored by the body as fat and muscle (and other things such as new bone growth, etc.). the point is that this extra energy is converted to matter. that’s why people get heavier. the converse is also true.
this is an irrefutable scientific truth. it is absolutely 100% true. proven again and again and again.
now, it is true that the daily TDEE calculation is a potentially complex one, and even if your calorie intake remains the same (recognizing that there is built in error % for knowing the calorie counts in food), changes in BMR for a variety of reasons can lead you to think your energy balance equation is balanced when it is not, thus causing your weight to change over the long term at faster or slower rates than expected... but that’s not the same as saying the “3500 calories to a pound” general rule is not true.
remember, for our purposes, whether 3400 calories (of carbs + protein) or 3600 calories (of protein + fat) equals a pound of matter isn’t really relevant. the 3500 calorie rule is a rule of thumb. getting hung up on things like the thermic effect of a diet at various ratios of carbs/fats/protein is a case of not seeing the forest through the trees. you could of course account for those effects with a more detailed model, but you reach a point of diminishing returns in trying to get too much detail. for weight loss/gain purposes, the simplified model works fine.
Blow your snark out your butt. I know what a closed system is. You, apparently, do not. A human is not a closed system.
“the laws of physics apply to everything.”
Not when misapplied. A human is not a car, and your body is not a gas tank. Assuming, of course, you crap sometimes. You body does not use or store all energy coming in. There is a reason some people can eat very little and not lose weight, while others can eat a lot and not gain - and the difference is NOT exercise.