Two different encryption schemes and/or passwords seems like a bad idea to me, both from a code maintenance/security point of view and from a usability point-of-view.
Can you expand on "private keys in base-58 export format are great for swapping around" -- what's the use case? Who are you swapping with, and how?
Swapping around means storing a private key outside of a wallet.dat, either to be imported into another wallet.dat or another bitcoin client implementation. It's an interchange format, not a specific wallet implementation.
The format proposed here is an extension that allows an exported private key to be password-protected. Naturally, if it is to be interchangeable with another bitcoin wallet or another implementation, it shouldn't/can't be protected using the same password or master key as the wallet from which it came (if that wallet is encrypted). The initial use case is to allow someone to use vanitygen to generate an address, and securely store the private key until it is later imported into a client.
Anyway, I think this proposal is orthogonal to the encryption of wallet.dat.
If you would rather this format follow the same password-derivation and encryption scheme as the master keys of the bitcoin wallet encryption system, that's certainly possible. They're already quite similar, and until pixelglow came out and recommended PBKDF2, they both used EVP_BytesToKey(). I don't think the use cases between the wallet master key and a password-protected export format are quite the same though.