TLDR: after enabling Apple Mail Plug-in, DT3 must also be restarted, to facilitate importing an intact mailbox hierarchy
I am starting to archive my old email in Apple Mail to DT3. I used the “import” panel in the left sidebar and used “archive mailbox”. One important aspect is to preserve the mailbox structure. Initially, this did not work; while the mails where imported, the mailbox structure was flattened. I realized that even though I had installed the DT Apple Mail plug-in, I had failed to enable it manually in Apple Mail (preference > general > manage plug-ins). I enabled it and Mail restarted. Everything looked good. Yet, the archived mailbox structure was still flat.
Solution: turns out that DT3 must also be restarted. After doing that, everything worked as promised.