I don't think you can force the transparency to display only your wallpaper on a system running Unity.
The reason can be found in one of the gconf
settings of gnome-terminal
on 14.04:
$ gconftool-2 --long-docs /apps/gnome-terminal/profiles/Default/background_type
Type of terminal background. May be "solid" for a solid color,
"image" for an image, or "transparent" for either real transparency if
a compositing window manager is running, or pseudo-transparency
otherwise.
The only way to get a pseudo-transparency (i.e terminal background set to the wallpaper) is by running Ubuntu without a compositing manager.
If your graphics card doesn't support 3d-acceleration, Gnome 3 automatically runs the fallback-mode (which is Kali's default mode). That's why you may have seen gnome-terminal
showing only the wallpaper.
Source: