Thematically, Guidance Chip has been a weird card to justify. My basic assumption, and I suspect that of most others, is that a specialized targeting system wouldn't care how many lasers a fighter is carrying when it is tracking and chasing a target. This confusion stems from the assumption that Guidance Chip improves the ability of a Missile or Torpedo to hit its target.
What if that assumption is wrong? What if the true purpose of Guidance Chip was to take over what the ship's pilot is doing during missile firing. Perhaps there are a number of tasks a pilot is performing in the cockpit to keep a missile on target as it zooms through space. Maybe he or she must paint the target with a radar, maintain communications with the missile, etc. Say GC takes care of all that mess. Now the pilot is free to do what pilots like to do: shoot other fighters with their guns. Maybe the extra dice modification from GC is not the warhead seeking better, but the contribution of a ship's blasters to the missile's attack, either by boxing in a target to reduce maneuverability or taking advantage of evasive maneuvers that may leave the target vulnerable in some other way?
This idea doesn't stand up to too much scrutiny, but it's the best I've got so far about why primary weapon value makes a difference in an ordnance attack.
