Our bodies aren’t 100% efficient when it comes to nutrient absorption anyway, so considering there’s a number of other factors at play, it’s probably making minimal difference.

When we eat, the food added to our stomachs signals the large intestine (colon) to get a move on and make room for incoming food. Caffeine can help stimulate this response, but since most nutrient absorption occurs in the small intestine, we’re not really losing anything of value. There is some absorption in the colon, but that’s mostly water being removed so we can have formed stools instead of chronic diarrhea.