https://oag.ca.gov/sites/all/files/agweb/pdfs/firearms/pdf/cfl2016.pdf?
Page 7: Handguns
California Penal Code section 25400 does not prohibit a citizen of the United
States over 18 years of age who is in lawful possession of a handgun, and who
resides or is temporarily in California, from transporting the handgun by motor
vehicle provided it is unloaded and stored in a locked container . (Pen . Code,
§ 25610 .)
The term "locked container" means a secure container which is fully enclosed
and locked by a padlock, key lock, combination lock, or similar locking device .
This includes the trunk of a motor vehicle, but does not include the utility or
glove compartment . (Pen . Code, § 16850 .
Without getting into the idea that someone somehow might make the argument that a single container attaches the ammunition to the firearm or that it might slip up against the firearm, etc., a separate container or even fixed dividers, etc., might be worth thinking about. the gray area though is what the locking boxes might be considered. This next one points out that carry to/from the vehicle is an area to be considered, too.
https://oag.ca.gov/firearms/travel
HANDGUNS
Pursuant to California Penal Code section 25610, a United States citizen over 18 years of age who is not prohibited from firearm possession, and who resides or is temporarily in California, may transport by motor vehicle any handgun provided it is unloaded and locked in the vehicle’s trunk or in a locked container. Furthermore, the handgun must be carried directly to or from any motor vehicle for any lawful purpose and, while being carried must be contained within a locked container.
Pursuant to California Penal Code section 16850, the term "locked container" means a secure container that is fully enclosed and locked by a padlock, key lock, combination lock, or similar locking device. This includes the trunk of a motor vehicle, but does not include the utility or glove compartment.