Installer for Windows (I assume you’re talking about Windows) is built with NSIS and supports NSIS options for the silent install.
GanttProject config file is named .ganttproject and GanttProject expects to find it in the user’s home directory. It is an XML file which you can edit in any text editor. You can make your own template and put it into user’s home directories when you install GP.
With respect to disabling auto-update, see this discussion: Need to disable the GanttProject 3.1.3100 update window