iptables - Correct. We use it for port remapping. We are removing this use in future releases.
rpm - Correct. Long term not everyone will use rpm.
Here's a little more back ground on why we currently chose to "fat pkg"
http://www.zimbra.com/forums/showthr...?p=513#post513
We modify the config files of postfix/mysql/openldap, so our tools that look for those would have to be tweaked. Your also right that the zm* commands in /opt/zimbra/bin are in some caes copies of the standard commands so you'd need to link or point to those if you have the dependancies installed in diffent places. We also modify cyrus saslauthd to auth against our LDAP, so you'd have to use our version there. I can't think of anything else at the moment.