Reyes was convicted of both illegal storage AND illegal transport because he did exactly what you describe. He was following the letter of the law, much as you and I understand it, and was still convicted by a jury of his peers. What has changed is that we now have some sort of precedent (not a good one) to guide us, whereas before we were all just guessing. (At least I was.)
The appeal will be interesting because it will either confirm that the storage and transport laws that we have basically make it illegal to keep a gun in your car at all OR it will vacate the lower court's ruling and give us a new (and better) precedent to follow.
IANAL, but I believe that there is more to it than that. I don't believe we are at risk for losing storage in a car, completely. You were responding to someone who kept their unloaded gun in a locked case inside the shallow rear storage compartment of his SUV. The prosecutors claim (albeit indirectly from what I have been able to view) that the glovebox was unlocked, and the defendents claim that a locked car should be sufficient. While it would be nice if the latter were the case, before this case most advice here has been that a locked car isn't sufficient; a locked case or container was required. If everyone agreed that the glovebox was locked, I don't think there would have been a conviction, especially as the jury asked about this very issue. However, the glovebox was apparently opened without a key, reading between the lines. Certainly, there is nothing in the case that suggests that a locked case would be a problem.
The whole carry issue (transportation) seems a mess here, as there is no evidence he moved the car with the gun in the glovebox. However, the glovebox is especially called out in the Federal Interstate Transport laws as not acceptable for "storage" during interstate transport. In addition, there is the whole "wingspan" issue regarding police searches, which would simultaneously suggest that someone could reach the gun, yet it wasn't in their "direct control." For example, the back seat wouldn't work. Again, though, this doesn't make sense in a setting in which there is no evidence that he transported the gun in any way other than what he claimed - in a holster, on his person.
Finally, it is interesting to note that the Internal Affairs officers who questioned him prior to searching his car asked him if he had a cable or trigger lock on the gun. Seems like, if he did, they didn't think it would be a problem. Suggests that it might be useful to keep a cable lock around for the time when you have to store your gun in the glovebox or console.