I don’t think I understand how the trimming could have worked: a manuscript without margins looks rather bad in general.
Some of the cases we are discussing (e.g. the Vicenza herbal) had annotations next to the part to be painted, in these cases they wouldn’t be covered by paint and they couldn’t be cut-off. Maybe the annotations were supposed to be scraped-off; or maybe it was acceptable that some of them remained visible in an average-quality manuscript.
EDIT: but I agree that it's reasonable to assume that many annotations were covered with paint and maybe trimmed, or scraped off, so the evidence we can see doesn't fully represent how common they were.
Some of the cases we are discussing (e.g. the Vicenza herbal) had annotations next to the part to be painted, in these cases they wouldn’t be covered by paint and they couldn’t be cut-off. Maybe the annotations were supposed to be scraped-off; or maybe it was acceptable that some of them remained visible in an average-quality manuscript.
EDIT: but I agree that it's reasonable to assume that many annotations were covered with paint and maybe trimmed, or scraped off, so the evidence we can see doesn't fully represent how common they were.