Interesting or possibly ironic as a side note to this discussion of side notes is the fact that this blog/site has apparently shifted to wordpress.com commenting after abandoning its own elaborate commenting system combining several plug-ins. I know this because a "related posts" link above shows me to the 2011 (ancient?) thread describing WPTavern's former commenting system (which displays quite poorly now).

Perhaps more directly relevant: the system used by Project Syndicate might be an interesting reference point. https://www.project-syndicate.org/commentary/j--bradford-delong-argues-that-the-us-will-face-a-dangerous-world-unless-the-federal-reserve-fulfills-its-global-role I don't see a credit for it anywhere, so I'll presume it's their own, not some 3rd party system. I like it better than Medium's, though it is in some ways similar.

Maybe it would be easier simply to add whatever JS bells-whistles regarding direct annotations on top of WP native commenting system. Could even be implemented via CSS w/o JS, or with JS only for aesthetics. In short, I wonder why it doesn't work as well to have 3 main choices for blogger: below-only, side-only, both-below-and-side, and then a user-option to show "annotations/in-line only," "general comments only," or "both annotations and general comments" in whichever location.