You can actually do this via the config.bat file. Simply click "Configuration Files" > Locate config.bat & click [ Configuration Editor ] for config.bat.
In that file at the bottom you will find "Code Outline", simply enter the following: -ForceAllowCaveFlyers into the box and click "SAVE" at the top left. Restart your server and then login to the server.
You will now find that you can fly inside caves.
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