You should read the sign and encrypt scheme in the context of people in cryptography and security industry determining the correct order for combining signing and encryption into authenticated encryption to allow you to send a signed secret message.
The naive sign and encrypt is any cryptographic scheme where the message is signed by the author's private key and then encrypted to the recipient's public key in the simplest, most obvious way:
message = encrypt(recipient public key, sign(author private key, message))
This simple scheme has a number of vulnerabilities, as described in the paper.
The other naive orders: "encrypt then sign" also has a number of vulnerabilities. In the past, cryptography API used to expose signing and encryption primitives, but not authenticated encryption primitive, so protocol designers and application programmers have always had to reinvent their own combining mechanism, which usually boils down to either one of the two naive ordering and the way protocol designers and application programmers combine these primitives often led to unexpected vulnerabilities.
The non-naive sign and encrypt would then be any authenticated encryption method that combines traditional signing and encryption primitives with additional operations that interlinks the signing and encryption operations, to avoid the vulnerabilities of the naive sign and encrypt. This is as opposed to true authenticated encryption that are designed from the ground up to satisfy the design criteria of authenticated encryption.
This approach of building authenticated encryption from traditional signing and encryption is tempting because if it is done correctly, it allows you to combine any signing algorithms with any encryption algorithms, and it may make analysis easier as you start with well known, battle tested primitives rather than designing totally new ciphers. This approach also has precedents, with high level operations like PBKDF and HMAC being built based on existing hashing primitives.