I do use fill flash fairly often and yes it does sometimes "spook" a bird but not always. The response to flash seems individualized. Some birds ignore it, some will "flinch" and not fly away while some will immediately leave.

The Better Beamer (or something similar) is key because of its ability to "focus" the flash at a distance....this allows you to use the very low power settings.

The low power settings offer a few advantages:

---refresh rate is very very fast and will keep up with short bursts of shots (but this might be more frightening to birds)
---the flash duration is very short so it aids in reducing motion blur
---battery life is extended greatly
---the images do not look "flashed"