I have some photography tools in a long canvas bag similarly sized to an AR case that hangs just behind/up against the back seats. I used the headrest studs on the top and cargo tie downs just below to stretch the bag pretty taut. ARs are short enough that it would totally work with a rifle bag/case too, and while it wouldn't be 100% invisible with the hatch open, it still blends in really well and I doubt you could see it with everything closed. You could even build a false panel to hide it behind, but I cant think of any better location than that one.

Also worth mentioning is that I have the whole back of the truck with 5% tint applied over the factory tint because I often have a lot of valuable camera gear onboard. The windows are BLACK. If instead I had a resident rifle in the truck I'd do the same. It's only a couple hundred bucks at a local tint shop.

Oh, and the gap everyone talks about is related to the stock cargo cover. There's a gap between it and the back seats to allow for the seats to recline. For your purposes it isn't relevant.