Yes, that's right, if you set this parameter to 'Off' in global php.ini configuration file it will affect every vhost.
Actually, as I know with data publishing for every site .htaccess files is uploaded which contains following information:
php_flag magic_quotes_gpc off
php_flag magic_quotes_runtime off
php_value mbstring.func_overload 4
It should work properly. But it won't work if you have PHP as CGI on your server.