Security through obscurity is more the concept that computer systems attempt to hide things in plain sight. Encryption/cryptography is an overt act of hiding data and, in essense, changing or encapsulating a piece of data. A good example is say you decide to fool attackers by running your vulnerable Apache server on Port 8001 instead of 80. You choose 8001 because you know no one else will run it there (creating a false sense of security). That is security through obscurity.

Another example would be putting your house key under the door mat because no one would look there.

Does this make more sense/clarify a bit more?