Michael Hopefully this sheds some light on your question:
Q1) The 'user directory' is the authentication source of the users such as LDAP, AD, SAML. Try a quick search on the regular Help site not the developer site and you will get some insight into what the user directory is: http://help.qlik.com/sense/2.1/en-US/online/#search-user directory
Q2) Since Qlik is not an authentication application we use other 3rd party applications to handle the authentication process. This is the first step for a user getting access into the system. After they are authenticated the Qlik application then handles the authorization to see what the user should have access to and what rights the user has in the application.