Why would the empires create these 'demigods' to roam the stars freely?
Why would they create something that can come and compete with them?
Why would they kill the people that they have trained?
Jeepers, this whole new development can get pretty restrictive and grimdark when you put your mind to it.
But basically it means, there is nothing that you can own, outside of what you have in your hangars.
Actually, quite a massive chunk of game mechanic starts to make sense from a certain point of view, including no crew / no visible NPC traffic, etc.
Basically:
Using an quasi-alien technology, you create a weapon that is overpowered, sentient, and (in most cases) has a mentality of your average criminal / teenager from a street gang / whatever. Quoting Hellgremlin, "a monkey with laser eyes". Of course, trained loyal officers would be much better, but only 1 monkey in a kazillion fits for the implantation, so we don't have a choice, and neither has the monkey.
How do you control these things, if there are thousands of them? How to prevent the monkeys from burning down the jungle?
Give it an illusion of freedom. Make it see only what it is allowed to see. i.e. "a banana on a tree from 50 m away only, marked by a red cross." Severely limit all contacts with baseline population or prohibit this contact altogether. No direct contact with its own crew. Separate egger-only areas in station. Separate market. A built-in device somewhere that, when activated, will generate that nice message "we're sorry, something happened (c) during a recloning process", etc. You'll never know if something really happened or this exact rabid monkey was terminated by the laser implant owner.
Make these things brew in their own juice, so to say. Unleash them in the wilderness to clear the pirates in droves, to colonize planets, to build their imaginary empires that last for an year, to fuel the =real= economy by providing countless manufacturing jobs. Make it so it's in fact totally impossible for them to do ANYTHING against the planetside populations of the empires except mopping up a few thousand unlucky red shirts here and there (marked by a Big Red Cross for easier identification). Control and direct it while letting the poor thing revel in its godhood.
Then, when you had enough, just press the Big Red Button and sent in the navy to occupy the area and to clean up / board all the dead capital ship husks.
It's Matrix meets Ender's game.
For extra sauce, make it so that the contact with the few =real= loyal trained officers who happened to be suitable for the pod and are legally employed by their respective governments, is also severely limited. Because they know what all this experiment is really about, they aren't former convicts or random civilians, and they don't play the Game.