So big things can be built out of wood.
Yes, but both buildings and boats have structural limits. For all materials, not just wood. The limits for wooden boats, even when reinforced with other materials, are known. The dimensions of the ark exceed those limits. Period.
When properly built, once the boards have received water and swell they will not leak as long as the boards stay in the water.
They're called planks. The issue with larger vessels is not their static integrity, it is their movement in a seaway. Small boats are not analogous to large boats in this respect for the same reasons that organisms with the dimensions of insects cannot be scaled up to the size of horses. As size increases the mass and resultant forces increase by a factor of 3 while cross sectional area (and consequently strength & resistance to torsional forces) only increases by a factor of 2.
Big wooden boats flex and open their seams.
Capt.