Does by right even exist in San Francisco? My understanding is all land use is subject to review and approval at the discretion of the Board of Supervisors.
What he's saying is that you can use land according to existing zoning code requirements without explicit zoning approval... Or you can convince the local Planning Commission to approve another use.
You would imagine so, but every permit that does not have a state-level override (for example, SB-35 of 2017) is subject to discretion of the Planning Commission. Which is an unelected commission with members appointed by the mayor or the Board of Supervisors.
From my experience as a planner and subsequent experience as an architect, I infer that the discretionary review process tends to prevent injunctive delays via the courts. Conclusion of the quasi judicial discretionary review process exhausts due process while direct decision by the board makes overturn by a court highly unlikely because the board has statutory authority to make the decision to issue the permit. From a project development standpoint, the timeline is predictable so long as it accounts for the discretionary review process. If discretionary review doesn’t happen then the project will be ahead of schedule.
To put it another way, discretionary review tends to benefit professionals but will tend to upset those attending their first rodeo. As I mentioned elsewhere it’s often worth hiring a local real estate attorney experienced at working with the planning department.