Hope this topic isn't too old to resurrect.
I suspect if anyone comes along looking for a solution to this it will be easier, instead of trying to find a configuration setting or PHP function that will work, to instead use the roundcube database.
All you would need to do to accomplish this goal is a) create a skin for each login domain, and b) create an entry in the roundcube database for each user as you create the user that adds the configuration setting for that user's skin. This is stored in the preferences column, which holds an array of all user preferences. If you add the row for a user when that user is created, then you don't need to try and parse that array to add to it, you can just set it with your initial user defaults. Like this, which sets the skin to "yourskin" and turns on the preview pane:
a:2:{s:4:"skin";s:8:"yourskin";s:12:"preview_pane";b:1;}
I, for one, use postfixadmin to create virtual domains, and the virtual domain admins use it to create users. It has a wonderful capability to have user scripts that are executed after a user is created. That can be used to insert the row into the roundcube automagically on user creation.