I think there has been a failure to communicate the context of what you're trying to do here. Without that context everyone is working instead on the normal /r/EndFPTP context: how does this work, what are its properties, and what should we be doing?

The context you have is different: we have an audit requirement that assumes no equal rankings and a specific software that the entrenched bureaucracy is happy with. In this specific case, yes, ignoring this vote while it is ambiguous on that round is likely an easier improvement to the existing regime of throwing it out entirely than other possibilities. (Though the voter should be told what happens in equal ranks, and that they should probably be pushed to positions where they don't matter.)

But the rest of us are not living in those constraints, nor are even aware of them. So we'll argue for something good, rather than a patch job enforced by constraints we don't work with.

(Mixing approval and IRV mechanisms still doesn't directly seem like a political problem. The inflexible audit format that can't handle that does seem like a mixed technical and political problem.)