The sad part is, we already have the technical infrastructure in place to support those user contributions - it's the Comments section of any blog-shaped site.
So called "Web 2.0" was all about readers contributing feedback to whichever content was being published through a channel. But the shape it took was not the original hypermedia vision, but a conversation of loosely related comments that could potentially go off-topic.
To support the annotation feature described in the article, it would just require that common web platforms allowed their current comment systems to attach comments to paragraphs in the article, and show these comments as side notes. Current moderation functions could be used to separate the wheat from the chaff. But it would require readers to adapt and learn to tap this resource to its fullest potential.