This discussion conflates comments with highlights, which are two different animals altogether.

The distinguishing feature of highlights is that they are anchored to a specific passage in a (hyper)text, which you want the bookmarking tool to make visibly distinct, searchable, and so on. Ideally you want this feature to work seamlessly across paginated texts as well as on PDFs.

Comments are an entirely different animal, and the way they do (or don't) interact with highlights will depend on how people use the site socially, which is not really within the control of the site author.

Binning bookmarks, highlights, and comments together as "content" is like calling wedding cake, bobcats and lighter fluid different kinds of "matter"; it's reductive to the point of uselessness.