So there's a way to play with the cheats affecting only your ships, but it involves some micromanaging. What you do is turn the cheats on, select all your ships one by one, and then turn the cheats off. Your ships will still be invincible the bad news is that the AI figures our real quick that it can't win that fight anymore and then just runs away continually in a single direction I used to be able to counter this with missile spam, but the infinite ammo cheat isn't working on my ships. To counteract this though I've been getting better at "chase' combat but it's still annoying watching a cruiser run away from a corvette beyond where the camera will follow.