@DustinB3403 thanks for helping out and resolving the issue! I cant thank you enough for the time you spent (remote-ing into the machine yesterday and helping all day today via private messages).
For the larger community it looks like if you create a new config.yaml file, XO will register that as config source and any changes after that is not taken into the account, you should use the default config file created by the script (i.e. /opt/xo-server/.xo-server.yaml) to start with or update the installation using the update script and then manually update the default config file.