In response to your question:

It is my understanding that vital records in Zacatecas
were burned in the revolution, but what about the Catholic
church records -- does anyone know if they were kept?

The Catholic Church records were the vital records in New Spain, New Galicia and then Mexico until the late 1800s when a secular civil registry was established and even then, it took some communities a while before they started complying with the government's decrees that all births and marriages had to be registered through civil authorities.

There appears to be a couple of Borondas around Jalisco and Zacatecas that are possible candidates for being relatives of your ancestor.  It is my understading that many of the Alta California pioneers in that time period were from the frontier provinces (Durango, Zacatecas, Chihuahua, etc.)

FRANCISCO XAVIER BORONDA  
  Male   Family 
Parents: 
  Father:  JOSEPH BORONDA  Family 
  Mother:  MARIA AVENDANO     
Marriages: 
  Spouse:  SEBASTIANA ANTONIA  Family 
  Marriage:  14 APR 1736   San Miguel, Cocula, Jalisco, Mexico 
 
FRANCO. MARIA BORONDA FLORIDO  
  Male     
 Christening:  13 MAR 1746   San Francisco, Villa De Reyes, San Luis Potosi, Mexico 
Parents: 
  Father:  JOSEPH BORONDA  Family 
  Mother:  JUANA MARCELINA FLORIDO  
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