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I would surmise that this is because Apple relies upon the PIN as a failsafe in the event that the Touch ID sensor can't / won't read your fingerprint. Let's say you only have your right thumbprint scanned and you injure it to the extent that it's no longer recognizable to the Touch ID sensor—what then?

Two-factor authentication would need to rely upon a much more reliable criteria than Touch ID.

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You could always set up one pin/passcode for two factor auth and then use a separate passphrase as a fallback to unlock the device. It woould be much better security that way.

Also while we are on the subject using a short pincode to unlock the device is asking for trouble. While the device ID is tied to the decryption and there is no way to extract it yet I have no confidence that it will remain that way forever. At which point the ability to crack a short pin off the device means the pin will get cracked in seconds.

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