I believe it means "flat" threaded email. You care about all messages that are part of a conversation, but you are not concerned about the exact structure of a conversation, so you list all messages of a thread in time-received order.
That is what I was afraid of. It did not make any sense to me why one would advertise to the HN crowd that even though the mail client may not provide the best threaded message display at least it does not provide the worst case scenario of flat sorted by date emails. I really wanted to like mailpile, but the email threading is terrible for serious use with mailing lists.
