It makes perfect sense since it adds a level of security, if your seed is compromised your funds are gone unless you use a passphrase, the passphrase for the backup is not your seed it is to decrypt the backup which has your seed, if the attacker gets access to your backup passphrase but not to the backup itself you are still safe. Of course you would never have the backup and the passphrase for the backup in the same location.
You understood correctly, but in this case the passphrase to restore the backup it is 12 words, the backup I believe it also includes the pin, duress pin, and brick pin.
Of course this makes sense. But using 12 words as a passphrase to encrypt the mnemonic code can be quite irritating. Especially for new user.
The passphrase can be chosen freely. Everyone can be free to chose 12 words or 11 or no words at all to encrypt it.
But generating a 12 word "mnemonic" to decrypt the actual mnemonic code is a not that smart approach IMO. Rather let the user set any passphrase.