In what world is a city deriving its charter from the state "dystopian?" Californian municipalities are wholly creatures of California state law. They derive their authority from the constitution of California, which grants them the power to enforce only "regulations not in conflict with general laws." If the California legislature wants to pass a law saying, "No more single-family zoning," the municipalities don't have a special constitutional right to ignore that, any more than they have the right to pass a law saying their residents can't sell a house to a disabled person, or that their citizens don't have to pay state tax.

There are some matters which are of enough interest to the entire state of California that the state narrowly prescribes how local institutions may interact with those resources. One existing example is the issue of water, which, as a scarce resource, is heavily regulated by article X of California's constitution [1]. Among other restrictions, article X straightforwardly makes water distribution a state concern: "The use of all water now appropriated... is hereby declared to be a public use, and subject to the regulation and control of the State." The consequence: if a city wants to pass its own particular water regulation, and the state of California disagrees, the city is out of luck.

Another issue the state might have a compelling interst in is the issue of housing. Like water, housing is a human necessity, and a scarce resource. This is especially true in the Bay Area, which is not contained in a single municipality, and which is thus subject to the rule of a number of governments whose competing and parochial interests naturally restrict housing supply in the entire region. Specifically, every locality wants to house the Bay Area's jobs, but it would prefer that neighboring localities house the Bay Area's people. The state of California is the only legal actor capable of fairly adjudicating this issue in such a way as to further the interests of residents of the entire region. This is why it would be perfectly legitimate for California to write laws forcing Bay Area cities to abandon overly restrictive zoning regulations.

[1] https://leginfo.legislature.ca.gov/faces/codes_displayText.x...