Is it possible to have the Mail App re-sort Mailboxes (alphabetically)? I have an extensive hierarchy of Mailboxes, which works well for my workflows. Within a given Mailbox many of the folders (sub-mailboxes) are already sorted alphabetically, but new ones I create seem to go to the bottom of the list (or even elsewhere in the list!) and rather than move them one by one, it would be much easier to have Mail re-sort them!
What’s your mail service? I had a similar issue with Exchange/O365 and the problem was that I had my folders all in the inbox. Moving the folders out of the inbox resulted in proper sorting.
It seems that when I installed the Mojave update all of my Mail mailboxes were re-sorted alphabetically, which is a big help. Perhaps signing out of iCloud on my Mac and removing mail, and then signing back in might produce the same result.