Well, there was one long gun in the trunk, but not a rifle, and I can say that with 100% certainty from what is shown on the video. As for the longer video that shows the guys in the hazmat suits taking a second object out of the trunk, I doubt that is a weapon of any kind.
When they remove the shotgun, the officer handles it first to make sure that it is unloaded and safe to hand over to the crime scene techs. He does no such thing for the second object, letting the tech reach it and pick it up himself. That indicates the second object was not a firearm.
However, the video cuts in while the clearing of the weapon is in process...Had the other object been a weapon, it may have already been cleared...
I've owned a number of cloth cases of varying types...It just doesn't look like a case to me...