Well.. long time no see. Just have some time to optimize the site for better analysis.

According to the official tutorial:
1. Enable mod_rewrite in apache2.

2. Enable FollowSymLinks option, which is default.
3. Enable FileInfo directives. Edit /etc/apache2/sites-available/yoursite.com.conf, add:

4. Restart apache:

Updated Dec 31, 2015:
Enabling mod_rewrite rewrites all requests including the one used by mod_status. To disable this, add a rule to the .htaccess file.

Then, change its user & group attributes to prevent overwriting from apache.