To achieve 100% transparent panels within Ubuntu, this involves modifying the default theme (Ambience).
sudo cp -R /usr/share/themes/Ambiance ~/.themes/ sudo gedit ~/.themes/Ambiance/gtk-2.0/apps/gnome-panel.rc
Then comment out the following line, as below
#bg_pixmap[NORMAL] = "img/panel.png"
A theme switch (from System > Preferences > Appearance) is required for changes to be applied. Now setting the transparency on panels effects all areas 🙂