That's not a good argument. First, music is not speech. It doesn't require linguistic processing. Second, you can hear chords instead of individual voices, so polyphony can be perceived as shifting harmony, and it usually is.
It's incorrect to reduce polyphony to just shifting harmonies. Harmony is of course the constraint but the whole point is about intertwined voices - various melodies that your brain can process simultaneously. Music is not speech, but it's not that far from the language as it seems in terms of processing. When you hear 2 melodic lines at the same time, you're brain needs to encode them separately, in a similar manner to parallel speech streams.
The argument is not about "is polyphony shifting harmony" but about "does the brain encode two or more separate signals for polyphonic music." There's nothing that prevents the brain from encoding the whole thing in one stream, and taking that apart at a later stage. E.g., it might code music like "G3 over F, F3 over F, Em, A3 over Em, B3 over Em, C#4 over A7, etc."
It's not that it has to be like this, just that a mere theoretical argument cannot exclude it. And even then, musical perception has basically no relation to language processing.
I'm not so sure it's just perception involved. You're going along a street and can hear a violin playing. A melody develops, you establish a sense of tonality, can predict next sounds maybe. And then you also make out a recorder. Another piece, totally unrelated harmonically. Another stream to process, I would assume a brain can handle it (at least a musical one should).
I agree that language processing is different, but some similarities do exist.