> the site design was and how clearly communicated the problem they were trying to solve

I don't agree with either. Even after I enabled JS (no warning) and then after reading the whole page, finally realized that the implementation of popins was completely broken on Firefox and switched to Chrome to reread it (it doesn't help that the first 'link' is not a link†, and the link says it's 'broken' but it means broken in a different way from being actually broken so when you click on it and nothing happens, you infer that nothing was supposed to happen, which is why you were told it was broken...), I still couldn't understand WTF the problem was or how any of this could be remotely justified compared to an ordinary ToC and section headers or anchors.

† I'll just note that I have looked at many, many sidenote implementations (https://gwern.net/sidenotes) and the choice to make your sidenote/footnote link look exactly like a regular link is an... interesting choice.