But where and when is the crew supposed to go then? I don't remember a single episode where someone mentioned they were off to drop some logs.
Heck, imagine being a species that does this the normal way, dropping that unit like a real warrior. Not getting those breaks will put a constipated look on your face all the time!
In a lot of the novels they refer to the “refresher” where they use “refresher paper” and honestly I would be really disappointed to find that they’re still using paper to clean their butts in 300 years.
It's the computer's job up to the point where you get on Picard's "shit list". That's when the person being punished is responsible for beaming the poop out.
Can you imagine the federation kidnaps you, and as torture they just keep transporting more and more poop into your intestines. When you do poop, it just gets transported back to your stomach. Until you die.