Sure thing, the file you want to mod is ShipBlueprintDefs.xml, specifically DroneFighterBlueprint, GuardianFighterBlueprint, and/or AssaultFighterBlueprint blocks.

Note that the Assault fighters are small hulls, and the drones/guardians are tiny hulls. Also, you can't directly set the stats, but you can change their loadouts, and loadout order.

For example, say I want my drones to actually have armor and point defenses:

The base block is

<ShipBlueprint>
    <InternalName>DroneFighterBlueprint</InternalName>
    <ShipHullType>Tiny</ShipHullType>
    <Role>Interceptor</Role>
    <CanBeBuilt>false</CanBeBuilt>
    <RequiredComponentType>BeamWeapon</RequiredComponentType>
    <RequiredComponentType>SublightDrive</RequiredComponentType>
    <ComponentType>BeamWeapon</ComponentType>
    <ComponentType>BeamWeapon</ComponentType>
    <ComponentType>Shields</ComponentType>
    <AllRequiredMustFit>true</AllRequiredMustFit>
  </ShipBlueprint>

By adding these two lines, I can tell it to add PD and armor.

<ShipBlueprint>
    <InternalName>DroneFighterBlueprint</InternalName>
    <ShipHullType>Tiny</ShipHullType>
    <Role>Interceptor</Role>
    <CanBeBuilt>false</CanBeBuilt>
    <RequiredComponentType>BeamWeapon</RequiredComponentType>
    <RequiredComponentType>SublightDrive</RequiredComponentType>
    <ComponentType>BeamWeapon</ComponentType>
    <ComponentType>BeamWeapon</ComponentType>
    <ComponentType>Shields</ComponentType>
    <ComponentType>Armor</ComponentType>
    <ComponentType>PointDefense</ComponentType>
    <AllRequiredMustFit>true</AllRequiredMustFit>
  </ShipBlueprint>

Keep in mind that hull capacity (as modified by techs and race traits) dictates exactly how much can squeeze into the ship.

If you want to make it so that different factions use different fighters, you might want to look at ShipClassDefs.XML. That file defines (racename)AssaultFighter, (racename)DroneInterceptor, and (racename)GuardianFighter (as well as the other core ship classes) for each of the base-game ship styles; I expect that if you pointed those entries to a different blueprint in ShipBlueprintDefs.XML, it'd change what fighters popped out of the carrier module.

The entries in ShipClassDefs look like

  <ShipClass>
    <InternalName>TerranAssaultFighter</InternalName>
    <DisplayName>TerranAssaultFighter_Class_Name</DisplayName>
    <Description>TerranAssaultFighter_Dec</Description>
    <ThumbnailOverride>Temp_Terran_Knight_Alpha_01.png</ThumbnailOverride>
    <ShipHullType>Tiny</ShipHullType>
    <ShipRule>Balanced</ShipRule>
    <ShipDesign>Terran_Knight_01T</ShipDesign>
    <AIShipClass>Interceptor</AIShipClass>
    <StrategicIcon>Knight</StrategicIcon>
    <BlueprintDef>AssaultFighterBlueprint</BlueprintDef>
  </ShipClass>

The highlighted line should be what you'd change if you wanted each ship style to use different kinds of fighters. You could, for example, take Sansloi37's guardian drone with armor blueprint and call that the BorgDroneFighterBlueprint and use the ShipClassDefs entry for the BorgGuardianFighter to give the Borg a fighter which differs from the standard (though you will need to ensure that there is a BorgGuardianFighterBlueprint in ShipBlueprintDefs for the BorgGuardianFighter entry in ShipClassDefs to point to).

I have not, however, tried this, so I'm not certain that it'll work.

You'd have to do that for any new ship style. I rather doubt you'd need to do that if you're just changing TerranAssaultFighter to point to CustomAssaultFighterBlueprint rather than AssaultFighterBlueprint, however. I could as easily have said (racename)AssaultFighter as BorgAssaultFighter; it'd make no real difference.