My argument was (aside from paint damage on freight) I don't generally worry about damaging chains. I'll use corners or padding to protect what I'm hauling, I've never used anything to protect my chains.
I think your normal practice is fine. I think a particular set of unusual circumstances bit you. I'll bet the chain turns out to be fine. I'd guess there was just something harder than the chain in the mix and then the tire and continuous movement turned that into a thousand miles of constant filing motion.
Either way, you have to replace the chain.
Good on you for being vigilant and checking things.