Those won't go away. They might be mitigated, but once again, you can only mitigate the portion that is due to driver error, and the major problem in those scenarios is physics.
The shock wave phenomenon is one caused by physics (it literally is modeled by fluid dynamics simulation), exacerbated by limited visibility, and exacerbated once again by human reaction times. You can only get rid of the human reaction times, and maybe a little bit of visibility due to communication (although I'm extremely skeptical that there is any incentive for cars to rely on wireless communication to make decisions).
Lanes merging is a physical bottleneck. Sure, humans might make the merge worse, but speed is still limited by the capacity bottleneck, not the friction of the merge. The zipper merge has never proven to be faster, merely safer and more space efficient. You'll get to the bottleneck faster, and cars that try to exit before the bottleneck will get out of your way faster, but that's about it.
