From scraping the forum, it sounds like the best way to do this is to make the world as you want in singleplayer, rename the save as default.vcdbs, then stop your server and replace the default.vcdbs on the host with the one you generated via scp or ftp. A couple people have mentioned how the server seems to ignore world configs from the serverconfig.json file once a save is already setup; by replacing the save with your custom one this issue is also avoided.