Multisite domain not working without symlink
I have the answer now. 

The symlink is necessary so two separate domains can share the one IP along with your server's records. Obviously the subdomains share the same name and so are fine just listed in sites directory. The symlink links the other domain or any number of domains to the same html folder where the root installation of drupal resides.

The clean urls for the symlink multi-site domain on my Centos 6.4 linux system running httpd require the default httpd.conf file in etc/httpd/conf to change AllowOverride NONE to All for directories. Then the service must be restarted for changes to take effect service httpd restart