The decision about which framework you decide to use depends primarily on who will be using FME Server resources. For example, if you are creating Internet applications and your web users are not in your Active Directory, you might want to use the default FME Server framework. However, if you are building applications to be deployed on your intranet, you might want to leverage your existing Active Directory to grant access to FME Server resources.
By default, FME Server ships with a built-in security module. Only FME Server uses this default security module and, as a result, it must be managed using the FME Server Web User Interface. All users and security information is stored in the FME Server repository database.