Legal Question in Criminal Law in California

They are not alleging that he had the firearm while stopped, but that at some point he touched the gun and had it near him so that he could pick it up. Possession means being in control of an object. If one of the other passengers had the gun in his possession and your son grabbed it and threw it out the window so that the police would not find it inside the car, he may have not been in possession but could probably be fined for littering, etc. But then the person in possession would have to admit to that, which is not likely to occur.

You presume that "possession" means "on his person at the very moment police apprehended him". That is not true. I possess many things that aren't on me at the moment, and so do you. And if I possess something illegal today but get rid of it tomorrow, that will not erase the crime I commit today. I can still be arrested and prosecuted for it in the future. Proving possession is easier when the defendant is actually carrying the contraband at the time of arrest, but in many cases there are other ways to prove it.

You have the answer to your own question. They saw him throw it out the window. That is possession in and of itself.