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I have not known Western Red Cedar (Thuja plicata), which is what I think we are talking about, have such a delicate root system. It is very similar to arborvitae and has a lot of very fiberous roots up near the surface as well as the roots below. I would not expect disaster by doing this on this particular tree. Although, I don't know how long it would take for those surface roots to cross over the sand layer.
Water will still get through, but it will not have the ability to pull all of the water out of the tighter capillaries in the soil above the bigger voids in the sand.
I have not done this specifically for this reason. I have isolated soil above another soil using sand before in small areas.
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