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This is more of a suggestion then an issue but unless I am mistaken, when creating a dedicated server, the server will use the settings from the main game. This is fine however what would be more user friendly is have it so the dedicated server uses separate config files from the main game.
This will allow people to be able to play on their normal version and change the world to whatever they like without affecting the server or having to remember to revert the changes before starting the server.
Feel free to discuss this or let me know if there is a way to do the above but from my current understanding, there isn't a way