On the other hand, once a sufficient percentage of cars on the road are autonomous, couldn’t they use cooperative navigation algorithms to improve throughput a whole lot?

There are so many inefficiencies with human drivers—chaotic merging, unnecessary lane changes, blocking of passing lanes, and so on. I could imagine that optimizing all those away would make a huge difference overall.

You could also probably increase speed limits. And fewer accidents should cause a significant reduction in traffic jams.