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Let me put this in equations. The basic equation is right:

      ES = CI - CO
ES (energy stored) equals CI (calories in) minus CO (calories out).

CI is all that you eat, but for CO we have

    CO = CO_physical_exercise + CO_excess_burned
The term CO_physical_exercise can be directly measured and is the same for everyone, given the same workload. But CO_excess_burned is different for everyone. E.g. we all know that person that can eat anything, do nothing, but remains slim. It is this term that deserves more attention.

CI also varies dramatically for the same food for different people. Because we don't burn food in a flame to release energy, we break it down using complex chemical processes which vary dramatically depending on the exact contents of our stomachs, our microbiomes, etc.

See https://www.sciencedaily.com/releases/2015/11/151119133230.h... for one example of this.

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