You should probably check the location of the .htaccess file with the rewrites against the path to the add-on as defined by your control panel. Also check the filepath for %{REQUEST_FILENAME} -- you may need to prepend /addondomain/ to it. Easiest way to see that value would be to do a test redirect, and read it from the address bar:
RewriteRule ^addondomain/(.*)$ http://www.example.com/$1?%{REQUEST_FILENAME} [R,L]
Everything depends on the rewrite code .htaccess file location and the actual filepaths that you are checking. They have to agree.
Oh, one more: In some cases, the construct
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_FILENAME}
is needed. Or in this case, perhaps
RewriteCond %{DOCUMENT_ROOT}addondomain/%{REQUEST_FILENAME}
It's rather inconvenient to test all of these possibilities, but you should be able to get it working.
Also, I'd avoid RewriteBase if possible, and just code the base into your rule. Not sure about using two RewriteBases in the same file...
Jim