Hi Manoj,
The main difference is as you have pointed out, the concept of encryption on database connection strings for automate.config on the app server. This was introduced in v6.7. The encryption is compulsory and is performed as part of the upgrade using your default encryption scheme. Alternatively, you can choose to encrypt using your own certificate post upgrade.
The process of modifying the automate.config should be transparent to you if you perform upgrade on the app server. You can also copy automate.config from one of your upgraded app server to all other app servers if this is the way how you wish to work.