Hmm. You DON'T get polyphonic output from a single pulse channel, that's not possible. Fast arpeggiation is a trick to squeeze a chord out of one channel but it makes a very distinctive rippled sound, often associated with C64 music. If you're talking about the warbling here, it's a vibrato effect.

But generally: the "main" voices of the melody are standard NES voices, while the faint backing chords (mostly represented as the thin little slender note lines scrolling downwards) are the expansion voices.

If you look at the waveforms at the very top, they're color-coded to correspond with the notes they're currently playing. The ones that say "2A03" above them are standard NES voices, while the "VRC6" ones are an expansion chip (same extra chip included in Japanese Castlevania 3).

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Thank you!!