I use Anderson flats, inside dimension is 16 x 16 x 5 inches, you can buy inserts that are 4 x 4 x 8 inches and fit 16 in a flat, or you can by the 2 x 2 x 4 inserts, which gives you 64 pots in a flat. The Andersons have mesh bottoms, and I often use the flat as a grow out container, holds roughly 3 gallons of potting mix. So I buy them in lots of 50 at a time, so that with shipping the each cost comes down to less than $10 each. They are very rugged, minimal flexing, they do flex, but with a little care you can avoid breaking roots of large individual trees.
Flexing of the container can break fine feeder roots which means if you use soft bags to grow out trees, you have to be careful about moving them around. Killed a nice pine that way once. Only thing that was done was move it around the yard without care to keep the bag from flexing. Dropped a few feet several times, by summer it was dead.