Why I think that the copyist(s)/scribe(s) did not fully understand the material

[Koen G]

That paper is rather misleading if you ask me. Not intentionally so - they are clear about their data. But from a historical perspective it makes little sense to compare modern books with a 15th century manuscript written on animal skin. Their list only includes 5 MSS from the 15th century, 3 of which were Fontana.

Did Fontana write without an audience in mind?

The vast majority of their collection is 18th, 19th, 20th and even 21st century.

You cannot draw any conclusion about what a 15th century book should be by looking at what people in the 19th century were doing. It was a different time, with a different idea of what writing can and should be, a different material culture, different social structures, different social norms and so forth.