We're pretty certain that the Scrambler will still earn the Trail Rated badge, since it has the four-wheel-drive, axle design and presumably the ground clearance of a normal Wrangler, which also earns the badge. That said, the photos from the forum do reveal some of the weak points one would expect from a stretched-out Wrangler. The lengthened wheelbase hurts the breakover angle and puts the rocker panels and frame at greater risk for damage. As pointed out in the forum, the camouflage looks pretty roughed up in those areas, and there don't appear to be any rock rails/frame sliders to protect it. The lack of them probably means this isn't a Rubicon model, as they're standard equipment on the Rubicon SUV models. If you plan to off-road a Scrambler, they're probably a wise investment.
The other weak point is the large hangover from the truck bed. This is an inevitability for having a usable truck bed, especially on a four-door truck. But it means the departure angle is much shallower, thus the tail end is at risk of being dragged and damaged. Looking closely, and it appears that happened with one of the trucks, as the bumper looks angled upward as though it got snagged on a rock or bent after hitting the ground.
These aren't risks exclusive to the Jeep Wrangler Scrambler, though. Any pickup truck taken off-road is going to have to contend with these issues. It's the tradeoff of having lots of cargo space and room for people, as opposed to the tidy little box that is the two-door Wrangler SUV.