If you want to set your own settings in the config section you can just do that, no need to include all the settings internally managed by ECK. ECK will merge your settings with the settings it generates internally, where your settings take precedence over anything set by ECK.
As to why you Kibana configuration does not line up with what you have in your manifest:
This seems relevant as it indicates that ECK was not able to update your Kibana deployment. So you are still seeing an old version of the deployment. Are you by any chance setting an empty Docker image or overriding the podTemplate for the Kibana deployment, in any way?
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