no, is not possible to change the location, you can do a symbolic link (ln -s …) in linux if you want to actually store the files in a different place, but if i understand what the issue is then it wont make any difference.
the risk of accessing documents directly is handled by apache (.htaccess) and most important by the application itself … is not really a “website” (i know what you mean, but there are substancial differences).
if you (or anyone) detects a bug , please report it to support@eramba.org