I actually almost mentioned this myself as a form of "level", but decided that it wasn't explicit enough in the navigation; I guess it would then have been valuable to just point out "maybe it should be a level". ;P
The analogy to this specific gap in a traditional forum is the category change between "on-topic" and "chat"/"meta"/"general discussion" (with then having the topics come below those section headings, followed by the threads, etc.).
> I have almost 500 HN "rep" and I still can't find any way to downvote.
(Someone else already responded to this comment, but for completion-sake and because I'm the person who called it out in the first place: you need 500 points before you can downvote, so you aren't quite there yet ;P. Downvotes on this site are pretty powerful, actually, so they thereby seem to be reserved for people who have deeply invested in the website, of which there are enough people versus the total amount of content posted that this isn't a problem.)
> There's not even any way to collapse branches here as there is on Reddit...
I agree that this is useful; it is a highly requested feature and I believe it offers a lot of value: it is, of course, an important feature of the explicit tree... within a single collapsed linear level, all content blocks all other content, and you are just screwed if you want to skip anything, as there isn't even a visual differentiator.
(That said, some of us use user scripts to get past this problem; I wrote my own, but there are a few on the GreaseMonkey archive site whose name I'm forgetting, as well as in the Chrome extension store. If the content didn't have the trees at all, you wouldn't be able to do this no matter how hard you tried. That said, again: most online community discussion systems, even the ones that claim to be flat, have trees at least 4-5 deep.)