God brought the animals to the ark, two by two, seven by seven (from the bible). I’m sure they were not trying to kill each other then (angels leading them in)and I wouldn’t be surprised if angles had something to do with keeping the peace on the ark. The ark and everything on it were protected supernaturally. I don’t know about the waste but maybe Noah and his family threw it overboard? Food? Maybe some kind of supernatural hibernation? Just guessing But I would guess I’m not too far off.
Some of the waste produced by some animals, think cow manure and birds for instance, could well have been used as food for others. Do not discount the hand of God in this whole undertaking, God created and could control the actions of all the animals in the ark. I agree totally with your remarks, God said my ways are not your ways and my thoughts are not your thoughts, at best our explanations are merely guesses.