Yes, it's a legitimate extra layer of security if you do what you're suggesting, but that's not what's occurring here, though it may be what's happening within AWS's own data centers. But again, let's not conflate the two.

From a customer's perspective: calling AWS will return the data unencrypted regardless of if this flag is on because AWS will decrypt before returning it, seamlessly. If the credentials allow access to the S3 bucket, that's that, and your data will still be compromised regardless if this feature is on or off.