Rename the cfg, StarMade will generate a new one if you in the right directory and restore you to defaults.
If it does so, then you may have messed up your cfg somehow, a mis-pelling or something like that.
You can now start over with the new cfg.
steam install is at: /Steam/steamapps/common/StarMade/StarMade/*
I 100% agree and endorse the idea of avoiding Steam for StarMade. Every time I have tried to update through Steam it has screwed something up. I've lost to many designs and it has corrupted to many galaxies, it just isn't worth the effort. Update through the StarMade launcher only and run the game manually.