I wonder if IEEE-754 designers anticipated this use case during development. Great article - this kind of "outside-the-normal-use-case" requires a very careful reading of the specifications/guarantees of the language.
IEEE-754 seems to say that NaN payloads are designed to contain "retrospective diagnostic information inherited from invalid or unavailable data and results". While NaN boxing in particular probably wasn't the intention, untouched payloads in general absolutely were.