It may be a violation. The property owner could have obtained a variance also. Contact the the building department and report it. If there is a violation, they will take care of it.
Have you checked with Building and Planning to see what their interpretation is? I take it you are not a land use attorney. You may want to consult with one, who may have the answer for you as a professional courtesy, or you may wish to refer your client to one who is well versed in the San Diego zoning ordinances.
This response is not to be construed as establishing an attorney-client relationship, and provides general information on the subject at hand only.
The first thing that you should do is contact the county. If you're correct about the building code, then the neighbors construction is likely illegal and the county will take action. As a general matter, a building permit is required to do construction in most instances. The neighbor is either building without a permit, or has been granted a variance from the zoning restrictions you mentioned. If the neighbor has been granted a variance, you don't have a legal remedy for a zoning violation.
You also will want to take a look at the county code to see if there is any procedure for neighbors who witness a zoning violation to take action.