The medium is the message — if the majority of people are interacting with a system via one of those mechanisms (say, threaded), then the conversations will look/feel thread-y.

You can see this on Reddit already if you look at live threads, which some subreddits create for live events, episode releases, etc. Typically, the mods will set these to sort by new by default, which leads to something that behaves more like a classic flat forum post, albeit sorted in the "wrong" order. These discussions tend to feel and behave quite differently from discussions in other Reddit posts, simply because the default UI is different.