I don't want a workaround either. I went to the Apple Store, and the Genius said there is no solution to this right now and to post feedback on apple.com. There may be a complex solution, but I wanted a simple one (i.e., defaulting to sort the mailboxes in ascending order, alphabetically). For now, you'll have to drag them into the right order. Or you could switch to a third-party email client (Thunderbird) or a web app (gmail or Google Inbox).
I use Google Inbox in beta, and it's working great! I'll send you an invite, if you like. I think web apps for mail are where we are going in the future of email management.
I've applied for an AppleCare representative position. See how good I could be? :-)