The whole thing is predicated upon supernatural intervention, which means that God can do anything to affect the story, but what God has decided to do in this case is make the story work well as literature, by behaving in an anthropomorphic way.

God could just snap his fingers and cleanse the world, but instead we get this literary narrative about boats and animals and floods.

Talking about the engineering of this wrecks that for everyone. I think that a) the creationists are wrong because they want to try to explain the engineering aspects of this, and b) those who don't believe the ark story are wrong to play along. Creationists can legitimately gloss over the details because God has made this work as literature rather than extolling his own talents at waste management, and those who don't think it's true or literally can't really comment on the story because it's predicated upon God being able to snap his fingers when it suits him.

God could have just suspended the need of the animals to eat or defecate for the duration of the trip, or just disappeared the waste, or whatever. It's one giant miracle and exploring any of this is about as fruitful -- for everyone -- as arguing about the physics of Harry Potter.