Hi, I created hnrss.org so I can take a stab at this:
1) Yes, adding `?link=comments` is the right way to switch the `<link>` RSS element from the submission URL to the HN comments URL. And since that's a global option, you can also do something like `/newest?points=25&link=comments`. Just join multiple parameters with `&`.
2) The difference between news.ycombinator.com/rss and hnrss.org/frontpage is `/rss` appears to be an exact replica of the HN homepage just as a RSS feed (so the submissions move around in the feed like they do on the homepage) while `/frontpage` is a reverse chronological feed of all HN submissions that currently have the `front_page` tag applied to it within Algolia.
(When Algolia indexes HN submissions, it attaches "tags" that can be referenced later. One of those tags is `front_page` which just means the submission is currently on the front page. See https://hn.algolia.com/api for more.)
Hopefully that clarifies why the two feeds appear to have different items.
3) While hnrss.org does have a `?points=X` filter, that's unrelated to `/frontpage`. Like I said, `/frontpage` is just submissions with the `front_page` tag while `?points=X` only returns submissions over X points. You can combine them, but you don't have to.
Hope this all helps!