I hate how in search results Fandom is always above the better wiki about the same topic, that are independent or on better wiki farms like Miraheze. Fandom's SEO is brutal. They've slowly crippled the website and fucked over the regular users, but that doesn't affect them does it? Pinned at the top of Google there are always more clueless losers cascading in, they can't lose.
An upside of linear threads is synchrony, you've pointed out. But the linear thread format isn't incompatible with nesting necessarily, with quoting you're effectively having soft-nested conversations. What's lacking is UX that emphasizes this mixed threading style, and thus benefits from the best of both.
It might surprise you that, I think 4chan explores mixed threading like no other website does. Threads are linear, but quoting results in backlinks meaning isolated conversations are easily navigable, filtering out the "firehose". There's also a button that looks like [-] that can hide a post and all its nested replies, this can hide a specific reply chain from the linear view of the thread. I gave the system a bigger eulogy over here: https://news.ycombinator.com/item?id=33567593
I can only think of Futaba-style discussion boards, that is, 4chan. On 4chan threads are linear, but you're supposed to reply to posts by mentioning their unique post nº. For example, the above comment would want to mention >>33566411 and >>33566389. You can mention as many posts as want. The posts get a backlink, so the thread is a navigable, true graph structure. Reading discussion on 4chan can be confusing as a deep chain of replies can branch out to mention a recent surface post, and to understand what's going on you have to both delve down focused reply chains but also be aware of incoming posts that are displayed cutting across any one discussion.
I chose to link a post where a picture visualizes a 4chan thread in a directed graph. Also, a screen above there's a "Thanks." to several other posts, in one post.
https://archive.org/search?query=miraheze