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.
Is it your impression that boats don't have compartments? Boats are designed, from the standpoint of both external shape and interior structure, to maximize their strength. "Not built like a boat" does not carry a positive connotation to anyone familiar with why boats are the way they are.
I still would like to know who determined the structural limit that a wood ark would be 300 feet long.
Shipwrights with centuries of experience behind them who did their damnedest to exceed it.