By default the settings are stored in the INI file %appdata%\IDMComp\UltraEdit\uedit32.ini and most users use the INI file. If you have detected that some settings you can configure in Advanced - Configuration except the key mapping, file associations, menu and toolbar configurations and color/font style settings for the syntax highlighting languages are not stored in the registry, please report them IDM by email. However, there must be an INI file that contains the entry to store/load the settings from registry and not the INI file. In the same directory as the INI file there are by default also stored the file containing the key mappings, the environment files with the templates, menu and toolbar profiles, the file with the column markers, the subdirectory with the wordfiles and some other user related configuration files. It is also possible to store the macros and scripts in this directory.
You could store all the files in the application data directory of the default user account which would result in copying them by Windows on new user creation to the application data directory of the user. But the problem is that the full paths to some files/directories are stored in the INI file and whether Windows nor UltraEdit updates them. So if multiple users use a computer and every user should have his UE settings, you have a problem because the user name in the path must be replaced in uedit32.ini after the account is created and all the files in IDMComp\UltraEdit are copied. Using environment variables in the full file/directory paths stored in uedit32.ini (or registry) is not possible. But UltraEdit sets the default paths if not specified in uedit32.ini. For example if uedit32.ini contains for the wordfiles directory just Language File= without any folder path, UltraEdit automatically sets it on first start by the user to IDMComp\UltraEdit\wordfiles in the application data directory of the user.
If a computer is used by default only by 1 user, there would be a simple solution. Put all the user's configuration files for UltraEdit in the application data directory of the "All Users" account or better any other directory where every user has full permissions and define a SYSTEM environment variable named UEINIDIR having the full path of this directory as value. As you can read in help of UltraEdit on page INI File Selection and Advanced Settings this environment variable is evaluated after evaluating the command line parameters before searching for the INI file in various directories. With this solution all the user's configuration files for UltraEdit are stored on all computers in the same directory (makes it easy to update them) and no setting must be stored in the registry. Some of the full paths in uedit32.ini like the macro directory or the wordfiles directory could contain a directory path on a server to manage them read-only at once. But I can't recommend that because configuration files on a server makes usually starting UltraEdit slower and the users can't work anymore when server is done. Better is that all users have all the configuration files on their computers and a login scripts updates them if necessary.