How do these apply to what we are considering here?

Which one? The high rents in SV? That would be Tragedy of the anticommons. The single resource is the land. The numerous rightsholders are the landlords and whoever profits from high rents. This assumes that zoning laws are the biggest issue and some people would argue against that.

The more general question was how free trade, where both trade partners voluntarily participate, can lead to bad outcomes. The answer is that a non-trading third party can be harmed and the environment can be harmed. Those Wikipedia links provide many examples.