Yes the mattress part "begins" after the forward hinge. Not sure if I understand what you're asking exactly, but with the current design you enter thru the rear of the truck.
Getting up to the bed is definitely a design consideration when working out the interior plan. If you had nothing in the back, you could put one foot up on the side rail and get yourself up that way. Since my dog sleeps with me, that wouldn't work for her getting up/down. In my truck (07 Tundra longbed), it's 4 ft from the level of the bed to the bottom of truck bed - too big a jump for her.
I wound up putting a raised floor in and then threw in a storage ottoman for the step up. Works for us for now, here's a pic, although this doesn't quite show what you're looking for because the canopy is closed:
Here's the view looking down from the mattress, with the canopy open.
Here's the sleeping area:
I'm always thinking about re-doing my interior to take advantage of all that space back there (5' x 8') and to get things more organized. Everyone does something different, I imagine that the JK answer will have to take into account the very limited space behind the seats, looks like it's only a couple of feet at most. Maybe fold down or collapsible steps?
I like the idea of throwing the cool AT drawers in like I saw on the SafariPacific ranger.