Several reasons:
- the accounts by Boone, Weitzman, and Craig
- the existing Alyea footage doesn't necessarily show the moment of discovery. At least the box that was allegedly over the top had already been moved.
- the existing Alyea footage is blurry and lacking in identification detail
- we don't know that exactly one rifle was found
- we don't know what did not get captured in the existing footage
This is from Alyea's account of finding the rifle:
Shortly after we arrived back on the 6th floor, Deputy Eugene Boone located the assassin's rifle almost completely hidden by some overhanging boxes near the stairwell. I filmed it as it was found. In my shot, the figure of Captain Fritz is standing within the enclosure next to the rifle.He is present when the rifle is found and filmed Fritz walking into the rifle "enclosure", standing next to the rifle. There is footage of this below. As you say, the Alyea film is very poor quality but it is a record of the discovery of the rifle, Studebaker taking pics of it, Day retrieving it from it's "hiding place", examining it with Fritz then dusting it for prints.
The clip below shows Fritz walking into the enclosure as Alyea describes. The image is poor quality but by his feet it is possible to make out the butt of a rifle in an upright position:
As I say, the rest of Alyea's footage concerning the rifle follows it through to Day dusting the rifle at which point it is possible to make out it is a rifle indistinguishable from the MC.