Sorry to jump in
I'm experiencing the same issue as mturillo on the multi-server setup outlined in the manual. PhpMyAdmin ends up on the webserver and is configured to connect to the localhost while the ISPConfig interface is creating client's databases on the dedicated database server.
I manually added my db host to /etc/phpmyadmin/config.inc.php like mturillo but you still run into the problem of clients having to allow remote access to the entire internet or knowing the IP address of your main ISPConfig server.
My first instinct was to change the defaults in the interface form (ispconfig/interface/web/sites/form/database.tform.php) and prefill the checkbox and IP address. Obviously kind of a hack that wouldn't survive upgrades.
I see in that same database.tform.php script it pulls the database server names out of the configuration. Would it make sense to automatically grant remote access to nodes configured as webservers? Leaving the remote access checkbox and IPs to servers outside of ISPConfig control...