I'm experiencing exactly the same thing.
Just after a default zimbra installation, when sending an e-mail, I was looking to the log file and that line came up.
2 Lines from my (unchanged - never edited) main.cf:
warning: do not list domain mail.example.com in BOTH mydestination and virtual_mailbox_domains
myhostname = mail.example.com
virtual_mailbox_domains = ldap:/opt/zimbra/conf/ldap-vmd.cf
So I suppose Postfix is getting the same domainname from the LDAP server...
Everything works fine though...
I don't think I should erase the setting after myhostname, but perhaps there's someone who knows postfix better?