The attached patch adds support for doing e.g.:
namespace { type = public prefix = Public/ location = mdbox:/var/lib/public/mdbox:INDEXPVT=~/mdbox/public list = yes }
So the private flags are stored in indexes under ~/mdbox/public/, while the shared flags are stored under /var/lib/public/mdbox/. The patch currently hardcodes the shared flags as only MAIL_SEEN. I'm not really sure what would be the best place to configure which flags are private. Perhaps a per-namespace default, but how to configure it per-mailbox?
Also per-user keywords aren't currently supported. And it's a little bit annoying that each private flag update must increase the shared modseq for the message, but that can't really be helped. (Alternative would be for each user to have their own private modseqs, which could get difficult.)
I'll probably commit this to v2.1 after some more testing.