For consistency it's important that mailbox drivers provide the same functionality. Inconsistency is especially bad when moving from one store to another (say, mbox to maildir) or use them simultaneously.
- $save_empty only works for mbox/mmdf, POP can't support it, don't know about IMAP.
- trashed files: we have $maildir_trash for maildir, $mh_purge for MH but nothing for mbox/mmdf (though searches on the indicate the X-Status: header has a "D" flag for it)
- there are tickets requesting to support more flags like "passed" (bounced/forwarded/resent) for maildir, etc.
For removing empty folders, there's a long discussion on mutt-users. Short: as it cannot be atomically, an implementation would contain a number of race conditions that cannot be safely handled. Thinking of MDAs as part of the delivery, it may even cause mail loss.
We should add $mailbox_trash and make the existing options synonyms for it and add support for X-Status: D (we do support X-Status: AF already). See dovecot docs (other sources mention the same flags).
We shouldn't probably support more flags unless they work for all mailbox formats. Inventing new flags for mbox just to support them breaks inter-operability with other clients. Example: #2460 is probably invalid.