"There must be some sense to it?"

There isn't. They are being stupid. Personally, I'd send them back as damaged produce.

Fortunately, the trees should recover from the damage reasonably well, except for maples and ashes (and others with opposite leaf arrangement) where there is likely to be a conspicuous permanent fork or kink in the stem.

Might be better to buy from forestry suppliers, they don't do this sort of idiocy.

Resin

Maybe the trees' buds are more susceptible to getting gnawed on? I planted several little trees last fall and all of them got their tips gnawed off by rabbits. Maybe they were preventing the inevitable hehe?

Maybe they wouldn't fit into the right size box for shipping?