Nested threading for long-running threads only really makes sense when you can manage the “read” status per post (as in Usenet and mailing lists). Otherwise, new “leaves” or subthreads in the thread tree are all over the place, and you don’t know which you’ve already seen/read and which you haven’t. Web forums generally only track a single “water mark” per thread for how far you’ve already read, which more or less implies that only chronological order makes sense. You still have hyperlinked indications of which post is replying to which other post, via quotes.

Mailing lists are a good example. For example take a look at some random threads from the Linux Kernel: https://lkml.org/lkml/2025/2/20/2066

If you reply to an earlier one, the UI will handle it and show a new branch where that conversation started. I'm not a huge fan of typical mailing list web UX and usually view flat, but it's so common that I guess a lot of people like it. My opinion is probably biased from years of using/running forums, so I'm much more used to that UI.

I think newer systems like Discourse will formally track replies to you (versus a new message in the overall thread), while legacy forums like PHPBB usually just quote-reply.