Steve you went a different direction that my suggestion intended. I'm OK with that, after all it is only a suggestion.
That being said...
To use the example of an incoming 20k kps missile being engaged by PD beam weapon with tracking speed 8k kps and fire control of 12k kps. Weapon ROF is 5seconds. As pointed out, under current rules there is a to hit penalty created by the differential between the 8k of the weapon and the 20k of the missile.
The intent was this: With enough time tracking a specific target (missile, fighter, ship, etc) the penalty created by the differential reduced or eliminated. To go into an actual bonus should require new tech (maybe some type of improved fire control)
I think the 'mechanics' of how to implement may be to invasive to the existing code though.
As an example from the POV of the user, When setting the PD mode there are additional options to set.
For area defense you still set the range to start firing, but you also have the ability to set a delay. The delay gets a reduction of the differential penalty. When the PD weapon fires one of two things happens: target is eliminated and the fire control resets and searchs for a new target, or the target is not eliminated fire control continues to track and reduce teh penalty until the next chance to shoot (delay still functions).
For final defense there isn't a delay per say. You set the range for firing, but also set the range to start tracking. In a similiar manor to the area mode the more time the fire control has assigned the target to the time it fires the speed diffential penalty can be eroded. But only if the fire control actively tracks the target.
The idea for the area defense could be used for the main beam weapons fire as well.
Basicly the difference between a snap shot and taking time to aim. Give the tracking systems more time to develope a better firing solution.
I think the concept is easy to envision, but I suspect that it would be difficult to incorporate with the existing code. I suspect that it's to contrary to existing logic to implement without a wholesale rewrite.