The carrying statute (131C) does not apply "once the defendant leaves his vehicle and leaves the firearm in it" (Comm v Reyes). It's about the only clear thing that came out of Reyes. So if they are going to go after him, they will have to do it with the storage statute (131L).
I would not be surprised if the arresting officer had 131C and 131L confused (as did the procecutor who went after Reyes and the people at EOPS who wrote their FAQ, quoted in Reyes). He might have believed that guns stored in the trunk need to be unloaded. If so, the charges will be dropped once the DA reads Reyes.
If they want to go after him for breaking the storage statute (131L), they could argue that the trunk itself is not sufficient for 131L because it can be opened without a key from inside the passenger compartment. Based on a federal definition, the court said in Reyes that "[a]t a minimum, to be secure, any qualifying container must be capable of being unlocked only by means of a key, combination, or other similar means."