Just one exception to your list of natural dyestuffs. I doubt the confederates used much butternut (Juglans cinerea) as a dye. The natural range of that tree doesn't extend much below Kentucky, the Alleghany Mountains of Virgina, and the mountains of eastern Tennessee/western North Carolina. The black walnut (Juglans nigra), on the other hand, grows in every state in the confederacy including every county in Kentucky, North Carolina, Tennessee, and Virginia.
I'd expect the term butternut came from the color of grey resembling the wood of butternut.