f17r multispectral images

[Koen G]

Could we at least agree that there's likely an intent to not make the marginalia as easily legible + meaningful as "Paint these green"? 

I agree that they are weird, much weirder than annotations in other manuscripts. You are right to point this out. In "regular" manuscripts, I am not always able to read the annotations, but I can usually see at a glance what it's broadly about, what the language is etc. 
Note that marginal writings don't always have the intent to communicate or even contain information. Sometimes they would write the alphabet just to test their pen.

When you talk about intent though, it reminds me of Hanlon's razor: You are not allowed to view links. Register or Login to view.
"Never attribute to malice that which is adequately explained by stupidity."

In this case, I'd say there isn't necessarily an intent to obscure. Maybe there is. But perhaps the marginalia writer did not yet master the language they were trying to write. Maybe they had not mastered writing itself, and made some mistakes turning the words in their head into written text.

One thing does look certain to me, which is that the three longer pieces of marginalia (f17r, f66r, f116v) are done by the same person, in the same way. Same handwriting, same flavor of weirdness.