A telecommunications carrier shall not be responsible for decrypting, or ensuring the government’s ability to decrypt, any communication encrypted by a subscriber or customer, unless the encryption was provided by the carrier and the carrier possesses the information necessary to decrypt the communication.
Note "unless the encryption was provided by the carrier." Skype is the one that provides encryption here (a carrier) as far as I understand. No user can influence it. You are right that they are allowed to make the systems where users would provide keys themselves and that then the carrier wouldn't be required to assist in the decryption.