> "Autonomous cars will clog up existing cities..."
Congestion charges. Limited licensing for TNCs. Dedicated public or private holding areas rather than "milling about". All of these have solutions.
> Meaning fewer "difficult" intersections, straighter roads, no bike lanes or pedestrian sidewalks.
It is already best practice in urban design to separate cars that need to quickly transit an area without interacting with it into completely independent routes where there are no bikes or pedestrians, and combine transit/bikes/walking into livable mixed mode streets where cars are not allowed. NotJustBikes has many examples of this, most commonly around Europe.
> To get anywhere one will need to hail one of those autonomous taxis and then zoom in it to a destination where it's again safe to walk in whatever pocket of human activity.
This is what already happens in places that don't have usable, safe, or car-competitive transit, modulo autonomous, including currently most of North America. The solution to needing fewer cars -- self driving or not -- is investment in transit and in ground-up overhaul of existing cities to optimize for transit and deprioritization of cars.