Noah's Ark volume calculation

What about aquatic animals?After all, many of them can't survive salinity and heat changes.And what about animals with very specific diets, like Koalas and Pandas?

You forgot something quite vital. And something that could lead to a huge number of deaths if done today in construction.To support 42,588 sq. ft. of 1 foot thick floors, you'd need a huge amount of support beams. Start throwing on animals and supplies and the necessary load bearing beams exponentially increase. It's not like you can just lay down 1 foot of 42,588 sq. ft. and then start loading. And it gets worse when the previous layer has to carry the load of the next floor. There's a reason why high rises today start with huge concrete foundations with massive steel support beams anchored to bedrock. The foundation for the Petronas Towers in Kuala Lumpur had something like 500 concrete truck's worth of concrete for their foundations (they poured from 12 midnight to something like 12 in the afternoon the next day, something truly insane). 120-meter foundations to be precise of reinforced concrete. You lose a lot of space to support beams, especially when the beams are made of wood which has a lower load bearing capacity then reinforced concrete, especially gopher wood. Much of that space, especially on the lower floors would have be devoted to support beams. That also increases the weight load resulting in necessary reinforcement of the hull.

The thing is the capacity of the ark is also dependent upon how it is built and how it supports the upper floors. You can't have just an open floor and expect it to hold its own weight much less animals and more floors above it. 1 foot for supporting timbers seems quite small given the square footage and how many animals we're talking about.

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There would be no problem engineering a wooden structure 50 feet tall.

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That depends on where it is located, what type of wood, what loads it was carrying and what stresses it would take. A simple structure not bearing loads and not having huge waves hit it every second is not a real problem.

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The supporting walls and the size of the rooms would determine the size of the beams. No floors or the roof would be a clear span. Everything would be supported by walls. The sides would be tied by the walls and floors.

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Agreed. That would severely reduce the total square footage.