Seems like most roof replacement work can be permitted over-the-counter; although the planning department states that historical properties or those over 50-years-old may have additional materials and processes. Curious to know how challenging the process is in SF?
My first thought would be "Yes!
If it is indeed one of the preservation properties, then more often than not - YES. However,it is easier if you do not plan to change roofing shape and switch to different roofing materials. Also, if current roofing situation is dangerous for tenants or people passing by which was registered by proper roofing inspector, then the process might go quicker.
However, not all of the houses over 50-years old are historical and if it is not, then the permit is over-the-counter as you stated.