Encrypting the home directory ensures the privacy of your data should someone get his hands on your machine. Under the same scenario, full disk encryption would also gives you the guarantee the system hasn't been tampered with.
What am I missing here?
If you are just concerned with identity thieves and basic asset protection then as long as that stuff is encrypted you are fine, whether that is whole system, home directory, ~/Private directory, or just those specific files.
There's no way to prevent anyone from tampering with your system, or even to make any tampering evident. The best you can do is a cost-benefit analysis and risk analysis of the different options.