For reddit, this is massively easier to implement, as each comment contains in markup an accurate timestamp.
That way the script only has to store the timestamps on which you visit a comment section, not the comment ids.
Additionally, that way you can select "highlight all comments since visit [...]" with a dropdown from which you can choose out of all recent visits you did.
Sadly, Hacker News does not provide any such metadata in the markup. (Just like the comment formatting is shit, and the markup structure is as well. HN should just copy the nesting markup and formatting 1:1 from reddit, and it'd be massively improved already).