Found solution for the above issue: Custom setting data is added via a post install script when we create the managed package. When creating a patch org, we have to forcefully run the class of the method used in post install script in the anonymous window. This will add custom setting data to patch org.

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While creating Patch Org, only metadata is included in the org while custom settings that are available in the original org are not included. Either I can use dataloader to add data or add it manually. Is there a way out by which I can include the custom settings data without using dataloader or  adding it manually?