Well, consider both the music and the manner of performance –
Musically: the Mothers and Beefheart vs., as FZ said himself, "a bunch of more-rustic-than-thou San Francisco white blues bands that weren't as funky as my little high school combo."
Peformance-wise: Zappa comes very much out of a Dada/absurdist tradition, and the kind of spectacles the early Mothers got up to (e.g. using the PA to play surveillance tapes of Bunk Gardner and his groupies while Ian Underwood runs through a Mozart piano sonata and Motorhead debates Jimmy Carl Black about whether they're commercial enough, or having off-duty Marines bayonet a plastic baby filled with ketchup) are a good deal more acidic and political than putting on your headband and junkshop tunic and singing about how feeling groovy will end the Vietnam War.
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