It seems to me that your idea of putting wood mulch over your root pruning box would work great! Especially, perhaps, if you temporarily covered the non-tree areas first with plastic or landscape cloth simply to make removal easier in the spring. If you did all this right after they went dormant, I think root pruning wouldn't be an issue over the winter, the plastic & wood chips all around the edges would keep the breeze out from beneath and protect the whole bunch from drying out & extra cold, and the uncovered top part where all the trunks were would be open to receiving all the healthy rain & snow. Without tunnels underneath the roots to make them colder and drier, anything you were growing that was already hardy to your zone I think would be completely fine even when the pile did freeze... since they are made to handle that much already, just fine.
Make sense to you?

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