Thanks for all the feedback on the proposed interactions between fighters and ground combat. I think I have now found a good way to make this work.
A new component, the Fighter Pod Bay, is similar in function to a small Box Launcher, except it will only hold Fighter Pods (see below).
Fighter pods are created on the Missile Design window. The various pod options, such as bombardment pod, autocannon pod and air-to air pod, will appear when the requisite technology has been researched. When one of those options is selected, the warhead strength field is replaced by a pod size field. The player can choose the pod size, with larger pods being more effective. The pod capabilities will be similar to the capabilities of equivalent-sized ground unit components, although the fighter pods have more flexibility in design. For example, a bombardment pod will have three shots, armour penetration equal to Racial Weapon Modifier * ((Tons / 20) ^ 0.6) and damage equal to Racial Weapon Modifier * ((Tons / 20) ^ 1.6).
Fighter pods are ordnance, in exactly the same way as missiles. They are built by ordnance factories, transported in magazines and loaded onto fighters. Unlike missiles, they are not expended when fired and will function during ground combat phases.
A fighter can be designed with fighter pod bays. Different pods can be assigned to those bays while the fighter is in a hangar, providing flexibility of loadout. The same fighter could be used for bombardment or autocannon pods, as long as the pods bays are large enough and the parent carrier has both types of pods available. The pods can be assigned to the fighter using the normal ordnance loadout.
Pods can also be assigned to normal box launchers, so a fighter designed for space combat can also be used for ground combat in an emergency. However, box launchers are three times larger than the missiles (or pods) they are designed to fire, while fighter pod bays are equivalent in size to the pods, making fighter pod bays are a much more efficient way to mount the pods. Because of this efficiency and no requirement for fire controls or sensors in ground combat missions, dedicated ground support fighters can be much smaller than their space combat equivalents. It is also possible to have hybrid designs mounting both pods and box launchers. Due to the requirement for smaller engines for dedicated ground support aircraft, ship engines can now be designed from 0.1 HS in size.