zappa does not tend to present women as less intelligent than men at all. in fact, the women in his universe are refreshingly real, in contrast to the women in much of the rest of the counter-culture. in zappa's universe, women have names, they have defined goals, they speak for themselves and they act independently of anybody's authority, often to the frustration of the men in his universe.
zappa also had prominent female members of his band, like ruth underwood.
what zappa's message really was was misanthropic. it was satire, of course. but, the core idea of his early work was not that women were stupid but that hippies were stupid. what critics tended to do was to isolate little pieces of his work, take them out of context and then present them in skewed and unrepresentative ways. it was really a hit/smear job, to the core - because his politics were threatening, and he had a really dedicated cult following.
it is no doubt true that very few of his critics really listened to much of his work. if they did, they'd realize that he presented male hippies as equally dumb.
rock music didn't really let women in as equals until the punk era. you're not going to find much 60s or 70s rock music that is more feminist than this, for example:
but, i'm going to request that you focus less on the female character and more on the satirical attack of toxic masculinity embedded in the male character.