Because they don’t want people who live in Ramona and work in SD using the coast road as a commuter route alternative to the 5? Secondly, one doesn’t want 50-60 mph traffic in the beach cities, since you have a lot of people (and kids) walking and crossing the road.
It’s unofficially called US 101, but it was de-designated as a national route south of L.A., so the towns can do what they like with the county’s permission. I think slower traffic in towns plus a 55 mph limit on the less built-up parts is a good compromise.
Also, from what I’ve seen, the choke point isn’t the road through those towns. It’s the fact that several bridges are under construction.