why not just use the original seed and a strong BIP39 passphrase? Surely this ends up effectively resulting in the same thing... a mnemonic string + passphrase?
Looks are deceiving. The extra word used in BIP39 is called "passphrase" but it is not encrypting anything. It also is not providing nearly enough security as when you actually encrypt something.
Take BIP38 for example focusing on the key derivation only, you can't even begin comparing the security that scrypt provides in BIP38 with what PBKDF2 provides in BIP39! For quick comparison the recommended iteration count used in PBKDF2 for security sensitive usages is 10 million; BIP39 uses 2048! Meanwhile costparam of 16384 used in scrypt is already more than enough, not to mention there is AES256 on top of that.