how were you able to buy one of their ships while at war?
I've honestly not had enough time to play with the ship mods to see what effects they clearly have, however in GC2 there were ship mods that affected the entire fleet.
I've been looking for similar mods and not finding them according to the text, but that does not mean that some of their ships might not have something that is creating a fleet wide effect.
That said, in my experience the AI always wins when equal tech meets equal tech... sooo yeah.