On the "crate" vs "boat" shape:
This is an area where Evangelicals are right and JW's are wrong.
Although the scales described in the Genesis story are unlikely, a boat shape is much more plausible. A rounded hull would absorb and spread out the force of impacts (i.e. waves) whereas a rectangular box would transmit those forces directly to the stress points (i.e. The corners)
That's why a bowl is stronger than a box of the same material (Which is something that can be easily tested)
We use width, height and depth to describe all manner of objects, from cars to trains, to airplanes, so there is really no reason to make that inference from the story to begin with.