I guess that another way to achieve the desired effect would be to run Firefox and your automated tests on a nested X server (xf86-video-nested/Xephyr/Xnest).
$ Xnest :1
$ export DISPLAY=:1.0
$ firefox http://something/to/test &
$ your-test-script
Since the nested X server has it's own idea of the focused window, moving the focus on your desktop shouldn't affect it.
(If you don't actually need to see the test progressing, you could use a dummy X server (xf86-video-dummy/Xvfb/Xfake) instead)