"Trees planted directly in the ground would be exposed to the same moisture levels as the trees in the pots, no matter how the water got down to root depth."
Simply not true and overlooks the obvious--the pot is the limiting factor here. Trees in the ground don't have their roots encased in a container with two drain holes that is itself encased in slower draining soil. All things being equal (unless you live somewhere like the Achafalaya swamp) the ground has infinite capacity to drain itself. The pot does not. Water will stand longer in the pot because the soil it in drains through bottlenecks--the drain holes. These bottleneck situation is complicated by the ground soil that's packed underneath the pot. It's like stuffing a clay plug into the drainage holes... It doesn't matter what the surrounding soil does (and ground water has infinite drainage capacity compared to a bonsai pot. It only matters that the soil in the bonsai pot can't get rid of water fast enough to prevent root damage.
Even landscapers recognize the danger of drainage problems when planting a tree. They advise making sure not to plant the tree too deep, include a raised central point and to poke holes through "glazing" caused by digging:
http://www.tree-planting.com/tree-planting-4.htm
I've seen people dig holes and store potted trees in them over winter. In spring they inevitably show the same kind of damage, sporadic dead branches and partial trunk die-back can be typical. Root rot and soggy soil are always present upon root inspection. Means there's been consistent water build up over the winter.
If you do want to store plants this way, GET THEM OUT OF THE POT and heel them into the ground. Without the pot, your argument is correct. You've eliminated the complicating factor in all of this--the container.