Koen Gh,
Searcher shows another example of the marks, on 43r, and they display the same sort of edges, although the irregularities appear even more pronounced on 94v because of the layer of paint. It is not possible to determine if these marks and the ones in 94v were made with the same tool.
However, as you mentioned the paint on the roots with the scratches is definitely different: the darker paint on the right side ones appears to have been added separately from the left side, either because the original painter ran out of the first color (or chose to use a different color for a reason), or because a second painter later added this.
All in all I stand by what I said, we have NO evidence of when this scratching was done, or even of when or by whom the underlying dark paint was added.
As a side note, I have checked Nick Pelling's book and the word "sgraffito" doesn't appear in there at all.
On his website, however, he does talk about "chicken scratches", and considers them as marginalia.
In fact in You are not allowed to view links.
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after one of the manuscript's re-bindings.
So there is no reference to Pelling's work that would reinforce the "sgraffito as evidence of provenance" theory proposed in this thread's title.
The so-called sgraffito on 49v is certainly an artifact of the manuscript's history, in the sense that it reflects something that happened to the Voynich at some point in its life, but it cannot be used as an indicator for provenance, simply because we don't know when it was made.