My impression, from reading about it, is that most book satchels were leather, but there were some book boxes that were wood.
However, as far as I can tell, these boxes were usually used after the manuscript was bound. But... my knowledge of this is superficial (I haven't researched it in depth), and it occurs to me there must have been some way to transport unbound manuscripts to the binder, as well.
Some images of book boxes, one of which is wood:
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If the worms ate equally in bottom and top covers, it seems that it may have been previously bound in wood. If they ate more of the bottom than the top, for example, then perhaps it was stored in a box.
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There were MANY different ways of stitching books. Probably each bindery had one or two preferred ways of doing it. Here is just one example of Coptic binding (wood?) and stitching:
Image credit: Gleasongleanings blog