Is the VM an autograph or copy?

[Koen G]

In my opinion, any scenario where the hole is made on purpose needs a good explanation. 

One possibility is that the hole belongs with the plant image. It's part of the plant's supposed appearance or symbolical meaning. Instead of drawing a hole there, they made a real one. There are examples of meaningful holes in manuscripts. I'm replying from my phone so can't look well, but this looks like a good example: You are not allowed to view links. Register or Login to view.

Another possibility specific to copying is this. Scribes would often draw images around existing holes (for example a grotesque face where the hole is the mouth). If there was an exemplar, an existing hole may have been incorporated in this way. The VM scribe, not understanding his exemplare completely, thought he had to reproduce the hole as well.