[DrScump]

  Nearly 98%(!!) of land in San Jose is zoned for single-family homes

You misquote your source (it says that NYT says that it is 94%, but that's hogwash given that far less than that is zoned for any form of housing). The referenced NYT article doesn't annotate a source.

More likely, the data says that 94% of precincts have at least one single family home.

Well over 10% of land is rights of way (e.g. streets, watersheds, etc.), easements, or is public property.

[muzz]

The link seems to indicate 94% of residential land in San Jose is zoned for SFH.

But even that could be misleading, since San Jose has massive city boundaries that includes hills and other places that really couldn't be built on regardless of what they were zoned for.