tcpcrypt just does the encryption part. Once the connection is established, userspace on both sides can invoke an ioctl that provides a session nonce. If the nonce matches on both sides, the connection is not man-in-the-middled. It’s easy to confirm the nonce matches: Both sides sign it and send it to the other party.
This has two big advantages:
(1) operating systems can opportunistically encrypt traffic for unmodified legacy applications and network protocols, allowing the endpoints to detect mass surveillance without requiring any certificates.
(2) Like newer versions of SSL, it encrypts the information currently sent in cleartext in the SNI, preventing the type of censorship in the article.