TG doesnt matter, only location and alliance status.
Area defence doesn't interact with or defend other ships at all; it shoots at missiles if they are within the specified range at the end of the round. It won't shoot at missiles that hit ships.
(A note with area defense; it occurs before normal beam firing, preempting attacks on enemy vessels in preference to attacking missiles.)
Another note is that you cant actually do area PD and switch to final fire PD at the last interval. I believe this is because weapon recharging happens after missile interception, so if a weapon is discharged via area PD, it won't have power for final fire until the round after next.