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?

Yes. Off the top of my head some factors which will affect this: bowel transit time, the general condition of the GI tract including the amount/efficiency of digestive enzymes, gut flora particulars.

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.

Certainly possible. In fact, I would expect this to be true for the same person at different ages: a 20-year-old who loses weight at a certain food/activity level would eventually become a 40-year-old who would gain weight at the same food/activity level.