How do I start with a clean Star System world on a new dedicated server?
Solution 1:
The issue I was having, which I document here just in case anyone else comes along trying to figure out the same problem, is that the dedicated server for Space Engineers seems to re-write its own config file whenever the server is shut down. This results in many of the changes you made to the config file being erased.
The procedure, which is poorly documented, is to stop the server entirely. Then make changes to the config files. Then start the server up again. "Restart" will never work.