Annotated Tools for Reordering: Commonplacing and the Space of Words in Linnaeus's Philosophia Botanica by Matthew Daniel EddyMatthew Daniel Eddy (Intellectual History Review Volume 20, Issue 2, Pages 227-252)
Müller-Wille and Scharf ‘Indexing Nature’, also points out that Linnaeus interleaved blanksheets into his texts so that he could take notes. Cooper points out that this had been a common practice in natural historysince at least the late seventeenth century (Cooper, Inventing the Indigenous, 74–5). 
Apparently interleaving blank sheets into texts was a more common practice than I had known! I’ve seen it in the context of Jonathan Edwards (1703-1758) using the practice to take notes in his Bible, but not in others.
Replied to Jonathan Edwards’ Organizational Genius by Dr. Matthew EverhardDr. Matthew Everhard (theLAB)
For all the help that Edwards has given scholars and pastors in the areas of theology, philosophy, and missions, it is probably due time that someone devote a doctoral project to Edwards’ organizational genius.
I’m particularly interested here in the idea of interleaved books for additional marginalia. Thanks for the details!

An aspect that’s missing from the overall discussion here is that of the commonplace book. Edwards’ Miscellanies is a classic example of the Western note taking and idea collecting tradition of commonplace books.

While the name for his system is unique, his note taking method was assuredly not. The bigger idea goes back to ancient Greece and Rome with Aristotle and Cicero and continues up to the modern day.

From roughly 900-1300 theologians and preachers also had a sub-genre of this category called florilegia. In the Christian religious tradition Philip Melanchthon has one of the more influential works on the system: De locis communibus ratio (1539).

You might appreciate this article on some of the tradition: https://blog.cph.org/study/systematic-theology-and-apologetics/why-are-so-many-great-lutheran-books-called-commonplaces-or-loci

You’ll find Edwards’ and your indexing system bears a striking resemblance to that of philosopher John Locke, (yes that Locke!): https://publicdomainreview.org/collection/john-lockes-method-for-common-place-books-1685

Annotated Jonathan Edwards’ Organizational Genius by Dr. Matthew Everhard (theLAB: The Logos Academic Blog)
Jonathan Edwards’s so-called “Blank Bible.” JE received as a gift from Benjamin Pierpoint, his brother in law, a unique book. Structurally, it is a strange animal. It is a small, double-column King James, unstitched and then spliced back together again inside a large blank journal. The result is a one-of-a-kind Bible that has an empty sheet between every page of Scripture text.
If one is serious about annotating a text, then consider making a “blank Bible” version of it.

Interleaving a copy of your favorite text can leave massive amounts of space for marginalia!

Copies of print and digital editions of Jonathan Edwards’ blank Bible are available.

Apparently one can buy modern copies of interleaved bibles as well: https://www.amazon.com/Interleaved-Journal-Hardcover-Letter-Comfort/dp/078524316X/

Video review of an interleaved bible:

What other books can be found in interleaved editions? Ayn Rand perhaps?