I came to the comments expecting more pushback but I'm surprised. What happened to the simplicity of reading articles without status indicators, link popups, notes, conversations, ...?
There's some of these that I think are overkill, sure, but I like the simplicity of some of them - sidenotes, progress bar, etc. Just little things that give you that much more information about what's going on. Gwern's page, to me, is too much.
My personal favorite mixture of style and implementation of these features is jefftk.com - simple, fast, but gives a ton of information in an unobtrusive way.
I also vote for turning plausible link targets into links, or at least giving them IDs so that they can be linked without cruft; and, ever so much, especially for posts in a group that are not consecutive, for links to the previous and next post in the group. I've seen some blogs that do backlinks but not forward links, which is very frustrating when they say something like "I'll finish discussing this topic in a further post when I have a chance" in a 2013 post, and now there's 11 years of archives to go through to find out whether they ever did ….
If it's not the kind of content you want to put on your site, well, don't. But they are they are there to inform you of something. (Well, except for the link preview. Link preview is not good. At all.)
The author's focus is on static-generated sites, so reader mode isn't super relevant since they don't have a bunch of junk to clean up in the first place.
OK, table of contents, you're cool.