I'd like to dispute the statement that there are only few signs of later trimming. Instead, in my opinion, the bottom edge of the folios has been systematically trimmed. That can be seen by the fact that edges of plant roots are in many cases trimmed (this can be observed in the Herbal and Pharma sections). In certain cases this looks like intended - like in f99v, - but in the majority of cases it does not. It would have been very weird to intentionally leave out tips of roots in a consistent fashion.
When I say "systematically trimmed", I rather suspect that the whole pack was trimmed all at once, or perhaps quire-by-quire, for which the most obvious reason which comes to mind is that untrimmed folios did not fit into the intended cover.
The latter means either that trimming was done when the MS was about to be bound into its present cover, or that one of its previous covers was of the same size that its present cover.
In this light the Q3 mark on You are not allowed to view links.
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The variation in the trimmed folio height (e.g. compare You are not allowed to view links.
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Login to view. which both appear trimmed) suggests that trimming was done over unbound folios - either one by one or loosely stacked. When you trim something already bound (e.g. a bound quire), you won't get such variation.