jpackaged applications support both system-wide and per-user configuration.
jpackage application launcher will look up the corresponding .cfg file not only in the application installation directory (the system-wide installation location) but also in user-specific locations. User-specific directories for .cfg file look up are:
Linux
~/.local/${PACKAGE_NAME}
~/.${PACKAGE_NAME}
macOS
~/Library/Application Support/${PACKAGE_NAME}
Windows
%LocalAppData%\%PACKAGE_NAME%
%AppData%\%PACKAGE_NAME%
where ${PACKAGE_NAME} and %PACKAGE_NAME% refer to jpackaged application name.