Your body doesn’t give a hoot about calories. Calories are not an accepted currency in our body. It does not count calories so why should you? A calorie is a calorie. So what? Who cares? Certainly not your body. Consider two foods of equal caloric value. On the one hand, you have a bit of sugary soda, and on the other is a plate of lettuce. Calories are identical. OK. So what? When you eat those two foods, does your body somehow measure these calories? No.
Your body doesn’t have a built-in Geiger counter either. Should we not care about radiation because our bodies don’t care about radiation? Should we dismiss rads as a useless metric and feel free to eat a high-plutonium diet or get ourselves gamma ray tanning beds? I don’t think so.
I will be the first to agree that lettuce and refined sugar are not nutritionally or metabolically equivalent, but it’s an illogical leap to go from there to the idea that measuring food energy is useless. It’s not the whole story, but that doesn’t make it useless.