RSS is, fundamentally, just links to web pages. Why would it need to have built-in commenting? Just go to the linked page and comment there.
Shooting comments off into the ether is fine by clicking the page and commenting there. But, if you have a couple of dozen blogs in your RSS feed, and leave a handful of comments a day, clicking back through the specific place to see if you've been responded to is way too much effort. Sites like HN, Reddit, and Facebook, have a central mechanism by which you can be notified.
In the '10s I had a blog with over 1000 readers, I had fewer comments, and less community than the replacement Facebook group has with a fraction of that number.
That may not be a problem for publishers who are purely interested in eyeballs. But that isn't all of them. If the aim is to free content from the walled garden (which I think is an important goal), then it matters.
I've noticed with HN it's very swarm-like and transient these days. Comment following is also difficult without some thread control. At a minimum you need collapsible threads. Too much to read, don't bother, say something that's been said already - and add to the noise. Or have a bypassed dangling leaf comment.
I've seen email notifications, but to me they are just as bad as subscribing to a lot of sites by email. That's kind of what RSS is for: aggregation. So yes, it means you don't have to click through sites, I accept that, but still not a good user experience. If you mean something else, let me know, I am interested.
I don't know what you mean by splitting the user base or constructing a parallel comment system. I'm just talking about how to provide commenting, as a content publisher. RSS + on-site page by page commenting (even with email notifications) has a fraction of the engagement (in my anecdotal experience) of FB.