Let me explain in greater depth.....
Actually internet works in this way:
When someone types http://www.abc.com
in a web browser, it will first resolve thru the DNS system to an IP address and then redirect the traffic to that particular IP (a web server).
And the webserver, assuming it is running Apache, will have a http.conf file, containing the information of the virtualhost, and then display the website in that directory. (this information of the directory is specified as the DocumentRoot of the virtualhost)
By setting a co-domain "abc.com", the virtualhost directive will contain a server alias, telling that both "abc.com" and "www.abc.com" are actually pointing to the same DocumentRoot, hence the user will see the same thing for both "http://abc.com" and "http://www.abc.com".
ISPconfig 2 supports easy setting of co-domain.
I don't see there is anything related to 301 redirect or what you called "duplicate domain issues"