But why not mix them together the way the IndieWeb has done?! A few people are using the new W3C recommendation spec for Webmention along with fragmentions to send a version of comments/marginalia/annotations to sites that accept them and have the ability to display them!
A good example of this is Kartik Prabhu's website which does this somewhat like Medium does. One can write their response to a sub-section of his post on their own website, and using Webmention (yes, there's a WordPress plugin for that: https://wordpress.org/plugins/webmention/ ) send him the response. It then shows up on his site as a quote bubble next to the appropriate section which can then be opened and viewed by future readers.
Example: https://kartikprabhu.com/articles/marginalia
For those interested, he's opensourced the code to help accomplish this: https://github.com/kartikprabhu/marginalia
While annotation systems have the ability to overlay one's site, there's certainly room for serious abuse as a result. (See an example at https://indieweb.org/annotation#Criticism) It would be nice if annotation systems were required to use something like webmentions (or older trackback/pingbacks) to indicate that a site had been mentioned elsewhere, this way, even if the publisher wasn't responsible for the resulting comments, they would be aware of possible attacks on their work/site/page.