"We measure food's calories by burning it" - are you sure that how it is done?

Humans (unlike say cows) do not digest parts of what is available in plants, which makes some vegetables filling and ultra-low caloric.

"we don't really know how many calories a given person will get from eating a given piece of food"

exact numbers of unknown, but difference is not so great, except truly extreme cases (and vast majority of fat people is not fat due to them)