Box in a box is very effective.
Filling the void in the box with packing material like peanuts helps prevents the crushing you experienced.
Also choice of box, some of the prio mail boxes are of a thinner gauge cardboard
and do not stand up to the abuse as well.
For plants in smaller diameter containers,
I would choose the prio mail triangle shaped tube/box,
more resistance to side crushing.
More rectangular shape a box is, the more susceptible to crushing.
These are very good tips, I have used packing peanuts before but only within the trees, usually just crumpled up penny savers to keep them from being tossed around, but the box in box also makes sense, when I have to transport plants in low temperatures (40 degrees or lower) I always place inside a garbage bag that I inflated then place inside a second bag that I inflate as well, different concepts but very similar for using the buffer space like a shock to reduce movement, I like this one a lot.
I always seem to forget about the cardboard tubes, these seem like an obvious choice for the size plants you talk about, very simple solution for those types of plants.