When every claim links to the notes that define it, support it or challenge it, a reader can stop at any point and ask the next question themselves. They are no longer limited to the order the author chose. You could go straight to the objection, or start with all the evidence/definitions that the author might have laid out.
It also lets a reader check how the author reached a conclusion. They can disagree with a specific step instead of dismissing the whole piece, and the author can see exactly which step was challenged. At some point, they'll also be able to reach out to the author to point out exactly what was missed and how they can cover all their bases.
The result is closer to a conversation than a lecture. The author has already answered the questions they expect, and the reader can see which ones were considered and which were not.