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Neither (A) nor (B) are concerns. In (B), the authors are just unfamiliar with HKDF. HKDF is a standard way to use HMAC for key derivation (RFC 5869).

(C) is the observation that you could lie and claim someone else's fingerprint (print it on your business card, for example). This doesn't accomplish much, but is a general issue with fingerprints (e.g. OTR, SSH).

You can try to bind more of the context (e.g. hash more identifying information into the session key or MAC), but this makes things rigid, particularly if parties might be contacted under aliases (e.g., imagine if SSH servers needed to be configured with all possible DNS names they might be contacted under, and rejected others).

But even then, you can't 100% prevent this - if the protocol "binds" the phone number, you can lie and claim someone else's phone number, or name, etc.

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