I definitely get these points and I do agree there’s a place for multi-level threaded discussions. Thinking about the difference, I feel like the best use cases for nested/threaded (e.g. in my experience certain subreddits and Hacker News) are often of the nature “many individual people reacting to a thing” more so than “group of people having a conversation together”. This can be great, but it usually leads to responses with lots of fragmentation, which is why it’s helpful to be able to easily read certain parts while collapsing/skipping others.
Discourse on the other hand is explicitly conversation focused, and the linearity is a constraint to try to enforce that principle. We might think of the structure more like a group of people chatting at a party. Folks can join and leave the circle over time (weeks later, even!) but it’s still basically a single conversation, that happening chronologically.
One important thing to consider is that these two different types of interaction come with very different paradigms in how they’re moderated. With something like Reddit or HN the mods main focus is typically making sure contributors aren’t breaking the rules. With Discourse, moderators have a high degree of control over actually shaping the structure of the conversations.
One example is that when a discussion starts to go on a major tangent it’s common for mods to split the posts of that tangent out into a new topic, to keep the original more focused. Along these lines, users can even “reply as linked topic” too if a post in a different discussion prompts some good-but-not-super-related thoughts.
There are other things you can do as a moderator to help keep discussions manageable, like renaming topics to have descriptive titles, closing topics that become stale / irrelevant, removing individual posts that detract from the conversation, etc.
Discourse is definitely used in all sorts of ways, and there are sometimes mega-topics that can be hard to follow. Conversation gets unavoidably messy sometimes. But I think at least when it comes to the aim of fostering good conversations it helps to keep things reasonably focused. Ideally there shouldn’t be too many cases where you want to read a topic but find it filled with a ton of distracting stuff you have to skip!