I found out that the <Directory....</Directory> in the flex-80.conf file is what is breaking the system. No matter what options you select in the webconfig, this just stops the pointing. I have deleted this and my site is working and the SSL is working too. It's just a pain that this is an autocreated file so I have no idea how long it's going to work for.

<Directory /var/www/html>
Options +Indexes -FollowSymLinks -IncludesNOExec
AllowOverride All
Require all granted
</Directory>