CA law doesn't directly address carrying a handgun on a motorcycle; however, it has to be in a locked container separate from the utility or glove compartment of a vehicle without a trunk. Argument could be made that the seat is the "trunk" of a motorcycle since you can't access the compartment while on the bike. Who knows?
I'd like to see a code reference regarding loaded mags. Here's what I found. It leads me to believe one could carry loaded mags in the same locked case, as long as they aren't inserted (attached to) the firearm.
12031. (a) (1) A person is guilty of carrying a loaded firearm when
he or she carries a loaded firearm on his or her person or in a
vehicle ....
(g) A firearm shall be deemed to be loaded for the purposes of this section when there is an unexpended cartridge or shell, consisting of a case that holds a charge of powder and a bullet or shot, [b]in, or attached in any manner to, the firearm,[/b] including, but not limited to, in the firing chamber, magazine, or clip thereof
[b]attached to the firearm[/b] ....