That it does, though I'd have to write a custom weapon script to avoid it. Since more often that not fighters are accompanied with missiles, and it's ammo regenerate, I don't think it's a big deal: at worst they are ready to engage new missiles as soon as they come close.
As for the carrier, the only thing that make the AI handle it is that you can't interrupt the firing. And with that long range, the AI try to keep it's distances. I really had to work around it's limitations but I think it turned out okay. And it better had to, because while super useful I don't think it's a ship very fun to fly yourself (it's so much stylish to blow stuff up in Tisiphone frig or Sthenos cruiser
).
Anyway, thanks for the report, and I'm glad to hear you are enjoying the mod!