So, for example, the protein from eggs vs the protein from oatmeal have different coefficients for the resulting kcals. [2:p25]
Of course, there's individual factors that matter and if you alter the food (cook it) you can also change digestibility and thus available calories. [3]
But I would think, based on how the USDA reference reads, that the disparity in digestibility between carbs and fats is somewhat accounted for?
[1] https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr13/sr1...
[2] https://www.ars.usda.gov/ARSUserFiles/80400525/Data/Classics...
If dieting works in controlled environments, the obvious conclusion is that dieting does not work in uncontrolled environment precisely because of the poor food choices, and because we, as humans, tend to discount the amount of calories in small things through out the day, nor do we rigorously measure.
All a "NEAT decrease" is saying is "people are more lethargic when dieting". It would be unsurprising if this were due to crash dieting, but this cannot "negate" a diet. Reduce calories further until the scale starts to move. Or be more active, despite lethargy.
It does not assume that every molecule is metabolized homogenously, nor that your body is perfectly efficient, and not even that everyone's body has the same level of efficiency.
It more or less means "track how many calories you are eating to get a baseline number. If you want to lose weight, decrease that number. If you want to gain weight, increase that number. Continue tracking until you establish a baseline number for whatever weight you wantwhen you have reached it".
Your digestive system generally does NOT "happily pass unwanted calories without absorption". Ingested fat is broken down into long chain fatty acids, which can be stored directly in adipose tissue with no further metabolic changes. If you consume a ton of fats at one time, there flat-out may not be enough bile salts released to emulsify it all down, and/or not enough pancreatic lipase released to turn all of the emulsified fats into fatty acids, and/or not enough time for them all to be absorbed in your small intestine. Statements like that are more or less like saying "Battletoads players will happily smash into barriers on bikes/surfboards/planes/clinger-winger", or "internal combustion engines will happily pass unburned fuel". It's a system in motion with a limited point of insertion (the common bile duct at the beginning of the duodenum), and hopefully long enough to finish the job. The fact that this is not always true just means that the system has been overloaded.
Gluconeogenesis from proteins is such a metabolically expensive process that your body does actually try to avoid that one, but it will if it has to, which is why rabbit starvation is true.
This post is peak overconfidence based on an amazingly shallow depth of knowledge.
But it's a very bad proxy for anything related to weight. Water is 8.8lbs per gallon and yet has 0 calories so you ignore your entire water maintenance cycle in the accounting. It also assumes that every single molecule of calorie-bearing food is metabolized homogeneously in your body which isn't the case. Your digestive system will happily pass unwanted calories without absorption (especially fat) and tends to store extra water along with carbohydrates (4x by weight).
It's a very simplistic idea that is only true in absolutes. It's a restatement of the 2nd law of thermodynamics which applies to literally everything and is so general and vague as to be useless.