Just discovered, it's based on some old school Micmix DynaFlanger. So cool! I guess Zappa used two of them in parallel on a lot of records. I've always enjoyed tweaking this effect, excited to finally examine this effect a bit deeper.
Here's a decent explanation of the effect, cheers! http://www.muzines.co.uk/articles/dynaflanger/8726
Looks like Pigtronix did a recreation for Dweezil as well, with a custom CV mixer: