the tag system-tray refers to the upper panel, and the panel refers to the upper panel.
So why do they both exist?
like this question: it has system-tray listed and not upper panel?!
The panel is the entire grey bar that spans the top of your screen. The "system-tray" is only the indicator area, where you have icons and stuff. In Unity, it isn't so easy to spot the difference, but in Gnome Panel, for instance, this area is a panel applet that can be moved around. The same is true for Xfce and LXDE, so in those environments, the difference is more noticeable.