More generally, I assume your reasoning here to be that actual food digestion is not a 1:1 to, say, food labels. Correct?

Yes, but more importantly, I ask whether the difference between "food labels" and "actual food digestion" may depend on the specific person. To use your example, some person may be able to better extract calcium from food than other person, either because their genes create different enzymes, or because their gut flora preprocesses the food differently.

Now apply this argument to the calories themselves. Is it possible that two people eat the same food, yet one of them extracts 1000 calories from the food, and the other extracts 1500 calories?

Define your 'work'.

Well, you have just returned my question. I was curious whether there are ways to spend calories that most people would forget to think about when thinking about "work".

For example, whether it is possible that we could observe two people the whole day and conclude that they do the same things (same kind of work, same kind of sport) and therefore their "calories out" should be approximately the same, while in reality their "calories out" would differ because one of them e.g. wears a warmer sweater.

Adding these two questions together, I am asking whether it is possible to have two people eat the same food, do the same amount of work and sport, and yet at the end of the day one of them gains extra calories and the other does not.