Clean way to add Theme specific editor options

Is there a clean way to add some theme specific editor options (configuration) in a way that neither a Wysiwyg module update nor editor update would overwrite them? For example if you wanted to combine CKEditor with the marinelli theme (see http://drupal.ckeditor.com/tricks), what is the cleanest way to do so (using Wysiwyg module)? I'm inclined to suggest new configuration field for such cases (see http://drupal.org/node/313497), so there would always be at least a dirty way to make such modifications without directly hacking the module/editor. A more advanced feature could be an API which would make it possible to supply an editor configuration with the theme.

NOTE:
Currently I'm searching for suggestions how to solve CKEditor + marinelli "problem" using Wysiwyg 6.x-2.1