But to my surprise, while I was trying to import an already existing CRM 2013 organization (database) of same server as a new one using CRM Deployment Manager 'Import Organization', it got the same warning.
Not sure what makes CRM to identify it as different version :) Reported it to product team, hope it will be addressed.
i.e. the UR applied in the CRM 2011 environment was not compatible for CRM 2013 upgrade.
You can only upgrade organizations that have Microsoft Dynamics CRM 2011 Update Rollup 6 or at least CRM 2011 Update Rollup 14. Upgrade rollups earlier than version 6 and Upgrade Rollups 7 through 13 aren't supported for upgrade.