Kalua, first keep in mind that the conf.d method I showed you is useful only for software that is the same across all the clients. For instance the client who owns mydomain1.tld uses the same software and configurations as mydomain2.tld for phpmyadmin. But drupal would have atleast parts of it be client specific. So in that case you have to integrate it into each individual client's webspace. So the conf.d technique won't work.
Also, with drupal I would definately say to use the multisite method if the clients are going to be sharing any of the drupal code. So, if they aren't going to install drupal for themselves in their own webfolder, then the multisite method needs to be used, and all folders such as modules, sites, files, etc that are specific to each site need to be located in the users /var/clients/clientX/webY/web/ folder.