The loaded shotgun ban was implemented to try and stop road hunting (at least I think that was the reason for it).
You can carry any other loaded firearm anywhere in your vehicle you want if it is plainly visible. If it is totally hidden (from all directions), you would have to have a CHP to carry it legally (regardless if it was loaded or not). Now that I think about it, the CHP Act only applies to handguns. Therefore, a rifle or shotgun hidden under the seat might still be considered carrying a concealed weapon. I'll have to check some more on that, but I don't have time at the moment. Maybe someone else knows for sure. I know if it was locked in the trunk or other compartment and unloaded you would be okay, but hidden, loaded, and not locked, not sure.