I believe there is an actual reply structure to threads -- replying to a post (via the quote button) is different from replying to the thread as a whole (which creates a new top-level post that can have it's own reply subtree). IIRC in profile options you can set up to view threads in reply mode (what email clients usually call "threaded mode") or flat mode (what I think everyone uses).
All this to say that it seems like it should be possible to get what Tym is describing.