While I haven't experimented with this yet, I suspect that the Domino XML toolkit can handle this requirement. Teamstudio Configurator can do a lot, but not change background colors for views or action bars, etc.
Here's a link to the XML Toolkit -- it's bundled right into R6, but is a separate download for R5. Go to http://www.lotus.com/developers/devbase.nsf/homedata/homexmltk
and you'll see what it can do, plus download the kit.
The basic notion here is to export an entire database/template design into XML, use standard "search-and-replace" to modify design elements, then re-import into the template.