1) ISPConfig is a controlpanel and not a webserver. It does not override any options.
2) There were all templates can be edited: /usr/local/ispconfig/server/conf/
3) By allowing overriding for options too. But never do this on a serverw ere you host clients or thye will be able to reconfigure your apache server and are not bound to the limits that you had set them in ispconfig anymore.