In order to work around this limitation I have created a PHP script that will automatically add header.html on the top and footer.html on the bottom of all html pages. The script also validates and fix the HTML syntax with Tidy (http://www.html-tidy.org/).
In order to use the script:
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Your server must support PHP 5
Make sure the extention php_tidy.dll is enabeled in your php.ini on the webserver
Unzip and place the enclosed files in the same directory as your html files on the server
Create a header file in RSD and name it header.html
Create a footer file in RSD and name it footer.html
Export/upload your new header/footer to the server
NOTE: If you already the htaccess file on your webserver, do not owerwrite. Merge the content of the two .htaccess files instead.
NOTE: The HTML validation/fixing by Tidy could break some functionality in your site. But if you are using valid HTML this should not be a problem.