[Martin CX]

I'm pretty sure there is an option for the administrator to disable threaded views altogether, but the idea, as it has been presented to me, is that the users can switch the format in which they view the thread as they please (probably by providing a link on the thread page).

As to your question I don't have an official answer. Personally I see two ways of handling the problem: One, that any answer that isn't specifically an answer to other posts in the thread is regarded as an answer to the first post in that particular thread, OR (two), that any answer that isn't specifically is an answer to other posts in the thread is regarded as an answer to the last post in the thread.