I think the gist of it is that aterms transparency is a pseudo-transparency so, instead of drawing what is actually just behind it, it draws what is currently displayed on the root window (i.e. right at the back). This presumably gets set by lightdm (though that's a guess).
If you don't change your wallpaper much, a bit of a bodge-fix would be to set your root wallpaper to the same as your XFCE wallpaper (which is actually on top of the other) with a program such as feh or nitrogen, e.g.
Code:
feh --bg-scale ~/Pictures/the_wallpaper_you_want.png
The downside might be if lightdm (or whatever) sets the wallpaper on every boot, but you could add the above code as an autostarting item.
Another alternative would be to use the XFCE terminal, as it supports true transparency (if compositig is enabled).
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