Ok, it seems that you can get both themes and extensions running with relative paths by editting the appropriate files. As Cusser mentioned, you need to alter any mention of an absolute path like this:
c:baseURL="jar:file:///X:/firefox/profile/extensions/GUID/chrome/package.jar!/content/package/"
And change it to a relative path like this:
c:baseURL="jar:resource:/profile/extensions/GUID/chrome/package.jar!/content/package/"
After you install an extension, exit firefox, open your profile\extensions\extensions.rdf file and make the changes above. After you install a theme, exit firefox and open your profile\chrome\chrome.rdf file and make the changes above. This will render the newly installed theme or extension portable.
Previous relative paths mention:
http://forums.mozillazine.org/viewtopic ... =30#570853