That’s because waste generally doesn’t contain any significant usable calories. If you’re passing undigested food then obviously it starts to matter, as abusers of laxatives know. It’s not typically discussed because it’s not typically a meaningful factor and if it is you should already know.

Yeah, crapping out calories is a time-honored tradition among people with eating disorders who don't like to vomit.

Your body doesn't care how the calories go out. If they're gone, they're gone. If you eat 3000, but crap out 2000, your body doesn't say "Yeah, well, that's not how you usually get rid of calories, so get fat."

Just because our methods of recording aren't perfect doesn't mean that the core idea is wrong.