By default, there is no duplication. sa-update will update only the stock rules. However, there have been additional channels created for sa-update to allow it to update the SARE rules as well. You just add the ones you want to your sa-update channels file.
One advantage RDJ seems to have is that it won't leave you in the situation of a non functional SA because your updated rules don't lint. If using sa-update for SARE rules, are these stored in the same location as the originals or are they downloaded to the /var/lib/spamassassin tree? If so is there a migration guide somewhere on moving from RDJ to sa-update? Alan