I can't find the pic. But a .50 cal ammo can fits upright under the center of the back seat in my 2012 Jeep JKU. Not that thats easy to get to. But there is alot of storage under the back seat. And I think if I painted it black to match the interior it might go un-noticed.

Both front seats have good sized pockets on the back. But underneath the front seats is pretty much blocked by manual sliding seat mechanisms. Idk if the power seats are any better. But I prefer more manual items on my vehicles than power. Bestop does sell a locking drawer that fits under them. But its a slide out or very deep at best. Which I don't know how easy the access is to get into them. 

There are probably mounted boxes you can buy for the rear seats. But I don't think the rear seat swivels up. 

The roll bars offer ample space for nylon webbed fire extinguisher carriers. And the same for holding led lights, holsters, flashlight holders etc etc.

But I have not looked closely for a space to hold a pistol lockbox or other pistol mounting location. I guess the bestop under seat box would work in the passenger side. But it requires a key. Which is slow and cumbersome. I do have a 5 button lockbox but it only holds one pistol and one extra mag. And is from a long time ago. I don't know what is available today. 

I think the seat back pockets are the best place for ifak. But my big concern with anything permanently stored is theft of course. For now my plan is a couple usgi improved duffle bags, covered with a black fleece blanket that matches the carpet, in the far back cargo area. Which is a huge area. But eventually I would like to build a false 6 inch or so floor in it. Cover it in matcging carpet. With a lock.