Earlier quoted context omitted.
If you eat 500 calories and burn 600 calories, the energy has to come from somewhere . So in a sense it is actually a pretty simple physics problem. It gets tricky because calculating calorie consumption is really hard (how much of what you ate was actually turned into energy) and calculating calorie expenditure is probably even harder.
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…
Also this is still calories in, calories out.