The new 3.099 version that I just put out should address the AI targeting exploits. That's when you send some transports (or whatever other ship) way off into deep space as an exploit to the AI targeting, or to do knowledge raiding at far too easy a level, etc. The 3.099 version harshly caps the speed of player ships that go out too far, making it so that players can go out infinitely but that it is unpleasant and unwise to do so, and they can't hide from freed AI ships by doing so. As much fun as I myself had with doing that, it was abusive.
In tandem with that, I also changed the transport reduction from 45% to 35%. After 2 hops that leaves you at 70% health, which still means you can't make a third hop without dying, but it makes it so that you can sustain 30% hull damage from other sources, rather than a measly 10% hull damage from other sources. Should affect the range capping as desired without making transports completely brittle again.