My limited (and long ago) experience with that calibre option set was clicking the '-' minimised it to the right/bottom end of the taskbar, but clicking the 'X' put it in state where it wasn't in the taskbar or in the tray, and could only be terminated with Task Manager or Taskkill. I recall someone posting that was because calibre can run as a server
I try to limit use of 'the tray' to tools that I run at startup because I want them at my finger tips (e.g. dictionary lookup, sticky note, clipboard manager)- calibre doesn't fit that criteria. I frown at applications that put themselves there regardless - e.g.Task Manager.
BR