Paragraph layout

[ololololo]

He's not too worried about the wasted parchment, it's going to be a family heirloom like the fancy local Lord has. Our hero has seen such works and is impressed, but of course he's spent his life with "working books", notebooks and almanacs and the like. So the influences of his design are naturally from what he's familiar with, but with an eye towards "fancy" works with one image per page like the books of hours etc. He even oversees the font he wants and every time he changes scribes he orders them to imitate the master font and page templates.

I'm not quite sure what you mean.
As I understand it, you are paying attention to the lack of paragraph formatting and the fact that the text looks more like a working note than a European manuscript.
In botany, "paragraphs" are clearly separated, and there is usually a space between them.
But I think it's better to look for examples of paragraph marking in balneology, where the text is continuous and not particularly "divided".
The marker there is p in most cases, t in fewer cases, k in even fewer cases, and only once f (on f78v, and then only in the word qofcheol). Some paragraphs, except for the first one, may start with s.
Apparently, the author did indeed separate paragraphs in his writing, often using the p-gallows, sometimes even making it into a betony. 
I hope I understood you correctly...