Read 12026.1 and 12016.2
These PCs are execption to PC 12025.
PC 12026.1 nutshell version = If while in a motor vehicle, the handgun is unloaded, and locked in a secure container, NOT the glovebox or utility compartment, it is not a violation of 12025.
PC 12026.2 nutshell verstion = If you are transporting an unloaded handgun in a locked container to or from any of the specified locations, you are not in violation of 12025.
PC 12026.1 is not overridden by PC 12026.2 so if in a motor vehicle you DO NOT have to be going to or coming from any specific place.
As far as the ammo and the gun having to be stored in seperate places/containers, there is NO PENAL CODE REQUIREMENT to store them seperately.
I carry my handgun (when not Open Carrying) in this. Full mags right next to the gun.