FWIW, I haven't encountered a problem with the revised setting on OS-X Mail v9.3. Initially, I did think something was amiss until I realized the "standard" folders had moved [SENT, ARCHIVE, TRASH, JUNK) in the default Mailbox list. Now, in the account specific list, only my custom folders appear. Plus it took a short while for the messages to appear. I'm no expert but I assume that had to do with indexing in the revised hierarchy.
I also use CloudMagic and have had no issues.
I have not yet updated my iOS apps to the new server addresses.
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