The numbers from research are that humans get over 95% of the calories from anything we eat, so for your 100kcal item your body gets approximately 95kcal of energy. The breakdown seems to be that we are ~98% efficient at digesting carbs, 95-97% efficient at digesting fats, and 90-95% efficient at digesting proteins.
This will vary a tiny bit person to person along a normal distribution, but that variation would be so small its negligible for the majority of people, the exception being medical conditions that affect your digestive process. For example, because lactose intolerance affects how the body digests lactose, people with this condition would get less calories from milk than someone without the intolerance.
These efficiencies are not included in the labels on foods, but are also not included in dietary recommendations. So when we say that on average people need 2,500kcal per day, you don’t need to do any math on efficiencies and can just add together what food labels say to reach that value. So if you eat that 100kcal snack, it counts as 100 against that 2500 target.
On the off chance this question was more than just curiosity, you should not need to take caloric efficiency into consideration when thinking about your diet. If you are in a position where these efficiencies matter you should be working closely with a dietician and not trying to do it on your own
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