Just like a custom toolbarset the theme also needs to be defined in the fckconfig.js and currently we have some limitation to changing it dynamically.
http://www.bitweaver.org/wiki/index.php?page_id=588&tk=bea0ce3999d89fd48f60&s5=1

Is there at least a way to define the background color of the toolbar and editable text area? How difficult is it to customize the FCKeditor lib to pass these value through?

The FCKEditor allows to define the css file for the Editor area using the config file.

Changing the style of the editor involves three steps:
1- Copy the fckeditor/editor/css/fck_editorarea.css file from the FCKEditor distribution and place it into the web app and make the necessary changes to the copied file.

2- Create a custom js file (e.g. CustomConfig.js) and make the following call into it.
FCKConfig.EditorAreaCSS = 'http://'+ window.location.host '/'+window.location.pathname.split("/")[1]'path to the css file' ;

Let say if the "fck_editorarea.css" file has been copied into the following folder "webroot/css", then the above call would look like this:
FCKConfig.EditorAreaCSS = 'http://'+ window.location.host '/'+window.location.pathname.split("/")[1]'/css/fck_editorarea.css' ;

3- No refer the custom config file using the customConfigPath attribute (e.g.)
<ice:inputRichText customConfigPath ="CustomConfig.js"/>

*3- No = 3-Now