If you were designing a new city from scratch, this makes sense. Much like in software, cities have "legacy systems" to deal with. In the case of homes in San Francisco, "air rights" had largely been priced into properties by way of historical architecture limitations (lack of elevators, then earthquake resilience).
What the zoning restrictions have done is serve as a mechanism to allocate air rights. Effectively, properties come with the air "in front of" them, not "above" them. This is reasonable, and consistent. I doubt anyone bought low-lying property in SF with the idea in replacing it with a skyscraper, but most people up on a hill definitely paid for the privilege. A shift in pricing of air rights would cause a dramatic market shift from the previously existing condition.
What the zoning restrictions have done is serve as a mechanism to allocate air rights. Effectively, properties come with the air "in front of" them, not "above" them. This is reasonable, and consistent. I doubt anyone bought low-lying property in SF with the idea in replacing it with a skyscraper, but most people up on a hill definitely paid for the privilege. A shift in pricing of air rights would cause a dramatic market shift from the previously existing condition.