There is no naturalistic explanation that possibly works. The entire scenario is absurd in the extreme. Suppose by some miracle this honeycomb structure didn't leak like a sieve as it flexed in the waves. You now have thousands of animals to take care of on a three level, "honeycomb structure" with one window. I assume you think all these animals are on cages in the honeycomb. How will 8 people take care of all these thousands of animals? Have you ever worked on a boat? I have. It adds many complications. Have you ever cared for horses, cows, goats, pigs or chickens. I have and under fairly primative conditions (no electricity or running water for instance) but not under anything like the conditions on the ark. Do have any idea how much waste these thousands of animals will generate and all of it dispersed through your honeycomb?
A single elephant can produce 300 lbs of feces per day. How much do you think the pair of indricotherium produced.
Indricotherium: Largest Land Mammal Ever - Associated Content from Yahoo! - associatedcontent.com
How about the Brontotheriidea?
Brontotheriidae - Wikipedia, the free encyclopedia
Not to mention all the other large land mammals and the dinosaurs and large permian reptiles like dimetrodon
Dimetrodon - Wikipedia, the free encyclopedia
Or do you think all these animals were extinct at the time of the flood story? Even with only modern animals it just won't work.
The story requires the presence of a lot of birds. Do you know that you can die from trying to clean out a poorly ventillated chickhouse?
Think of doing it on this big boat sealed with pitch during 40 days and night of global rain.
Then you have to have specialized diets for a lot of these animals and you have only 8 people to take care of all of them. This giant leaking, flexing, supposedly floating zoo would be a death trap for all on board even if it didn't sink the first time it encountered a wave.