Of course it's not meaningless. Those calories are energy. If I ingest 1800 calories, and burn 1400, but poop out 400, I will maintain my weight, despite not burning as many calories as I ingested. If I have gut bacteria that break down certain long chain sugars so that that I can now ingest them, I will instead only poop out 200, and start gaining weight, despite eating the same thing, and doing the same amount of exercise.
Well, the answer in that case is simple: eat less. The amount you eat should be determined by how much exercise you get AND by how efficiently your digestive system processes calories. If your digestive system extracts more calories from food than someone else, you need to eat less. It's that simple.