Federated comments/annotations sound really cool from a developer's point of view, but also seem like a nightmare for publishers. If you cede administrative control over the comments on your site, how do you control trolls/attacks/spam/etc.? Services like hypothes.is can do some filtering automatically, but this is missing the level above that - editorial privileges on comments on your own domain.
Ultimately annotation is something that readers choose to enable by adding to their browser, and by choosing the service they prefer-- just as they may elect to have a discussion about the page on reddit, twitter, facebook, etc.
With regard to whether sites should be able to have editorial privileges on their own domain, or to what degree should page owners have consent over annotation, we've blogged about that here: https://hypothes.is/blog/involving-page-owners-in-annotation...
There's a wide diversity of opinion. Some suggested a flag where site owners could register their preference not to be annotated. Overriding that flag would invite additional scrutiny from moderators. Others have suggested that such a flag not be able to be overridden.
We also facilitated a panel discussion on this discussion at our last I Annotate conference in 2016. https://www.youtube.com/watch?v=i2yFnu_pCGI&list=PLmuJEyeapl...