Maybe. I certainly don't think 'out' is just 'energy burnt' i.e. exercise, daily living - it's a complex interplay of factors. Maybe using a different word on here would be better - negative energy factors?
Out = anything that causes a negative to the energy balance, including as mentioned calories that are lost in poo (which are not insignificant) and metabolism (which is affected by the gut microbiome amongst other things), exercise, fidgeting and so on. Even thinking can cause more calories to be lost, interestingly (not much though!).
The reason they keep those patients on metabolic wards and try so hard to control all factors - even though it's borderline impossible to completely do that - is basically because of the energy balance.
I just wanted to touch on this because it's interesting:
"That is why you can't just say 2500 calories a day of microwavable Hot-Pockets with ranch dressing and a diet coke will lead to the same body as 2500 calories of whatever your great, great grandparents were eating. It is the same number of "calories in, calories out" but obviously not the same outcome."
If you want my thoughts on this area it isn't the same number of calories in or calories out. When you eat 2500 kcal of hot pockets your body doesn't absorb 2500 kcal. Likewise when you eat 2500 kcal of nuts you don't absorb 2500 kcal. Calories in doesn't literally mean the number written on the packet, in terms of energy balance it means the number of calories your body absorbs/extracts which is different depending on the food. Some foods also take more energy to digest (so adding to negative energy factors/out), some have a higher % passed out. Those figures are estimates and averages at best. It actually isn't the same number of kcal in (to your body) or out (negative energy factors) either. The true numbers (in terms of your body) aren't the ones written on the packets. Those are usually done by combustion studies or now the Atwater system (average values of 4 Kcal/g for protein, 4 Kcal/g for carbohydrate, and 9 Kcal/g for fat) - which were actually calculated by using combustion/averaging. This is not your body!
It's a lot more complicated than that but I didn't really feel like writing more of an essay. Hope that was in some way interesting or at least relevant to the hot pocket dilemma.