The author goes into the correlation between categorization (branching) and the use of the index and the focus on them respectively. He mentions he "learned" that branching would be more beneficial than the using of the index to make finding the cards easier.

I strongly disagree with this focus. I agree with the "relational" principle of put the card between the one that has the closest proximital conceptual relation. The Zettelkasten's power relies in serendipitous creativity (or creativity/insight by chance), this is facilitated highly by the use of connectivity between cards, where each card as you go down the "hierarchy" of "branches" will be more unrelated to the original topic. (See also Luhmann's paper Communication with Zettelkasten, Manfred Kuehn Translation and Johannes F.K. Schmidt's article on Zettelkasten within Forgetting Machines, as well as his video presentation about Zettelkasten). In short, the friction of searching for cards by following trains of thought through connectivity boosters insight by chance and therefore facilitates the power of the system.

This is also, I believe, why Bob Doto argues to let categories emerge after the creation of notes/streams of thought instead of making the names for the "branches" up front.

I believe Luhmann himself also emphasized the use of the index by calling it a system of "query into the database," the index is the main navigational map for the Zettelkasten. If you have a question for your "communication partner" the index is the way to go. For example, if I wanted to know the impact of cognitive load theory within employee management as a CEO, I would go to my index and collect the entrances for both "branches" or terms, and then start reading these thought streams... Afterward, I might synthesize and create a new branch somewhere, in one of the aforementioned categories, or an entire new one, where I put the results of this questioning.

My own system of numbering and branching in this way is the following: A number signifies a note's position within a stream of thought. I branch off if, following the relational principle, a note adds unto a thought on a specific card, but not the stream specifically. This gets signified by a letter.

So, 1a1, 1a2, 1a3, and 1a4 are all part of the same stream while 1a, 1b, and 1c would all be different "branches" stemming from the original card that would be 1 in this case. This can repeat infinitely, therefore facilitating what Luhmann calls "Infinite potential for inward growth" of the system. It's autopoietic and cybernetic. (See also: The Radical Luhmann by Hans-Georg Moeller).

Something that can benefit the finding of notes once the system grows sufficiently large is the use of "structure" or "hub" cards where you put down a few key entrances to concepts related to this stream of thought or "branch" in remote sections of the Zettelkasten.