Typically the passenger compartment is highly reinforced, and the rest of it is meant to absorb energy. I would expect that the strong passenger cage would also be stiff, and they could use the same materials and design tools to make sure it flexes in a desirable way. What I'm trying to say is they have the technology they need to make a unibody that can withstand off road use, even if current designs are not quite good enough. Jeeps aren't exactly known for great design or quality in my opinion, and I'm sure Toyota could do better. If fatigue isn't a problem for a ladder frame then it shouldn't be a problem for a unibody either.
First off, they do have the technology; that's why most every professional/hardcore off-road rock crawler/desert runner tends to be "unibody" in the sense that it's a full tube frame vs. Body on Frame.
Yes the cab is "stiffer" and more structurally sound against compression, rollover, and impact; but that does not translate directly to being able to be more robust when it's being twisted laterally and longitudinally. Those are forces not typically seen or expected in an accident, nor is on-road twisting/flexing as severe as you would see when rock-crawling. The stiffer you make the unibody, the less comfortable it will be on the road and the more effort and manufacturing you end up putting to make it handle like a BoF vehicle and less like a unibody.
You're statement regarding that if a ladder frame handles torsion and fatigue good, then a unibody should is flawed. The ladder frame is an entirely seperate section of the vehicle than the cab that bolts on top; it stands up to torsion and flexing so well because it's a very simple design that is strong but not overly rigid. When the frame twists, most everything bolted to it can give a little without causing issues; that's why the body is floated on the frame with rubber bushings. When the vehicle frame flexes that torsional force is not directly transferred to the body because it can wiggle on the mounts.
In a unibody you do not have that luxury, when one corner of the vehicle twists opposite of the other, the forces act on everything, from the suspension mounting points, through the body rails, and sheetmetal, ect. to the other corner in the vehicle (where as in BoF that's isolated into the ladder frame) Everything is attached and supported by the unibody, where as in the BOF the frame and cab are isolated from that type of torsion for the most part.
You mean the unibody 1996-2004 Pathfinder? Those were arguably the best generation of Pathfinder, especially with the VQ35 and manual transmission combo. The unibody Jeep XJ is highly regarded, though one of the weaker examples when wheeled hard. Land Rover has also proven that unibody is capable.
Depends on what you mean by capable, the thing I see most commonly is that after a certain point those unibody's need to be reinforced to survive. So then you start seeing owners weld/bolt in bracing, after that doesn't do as well they'll go full exo-cage that strengthens the vehicle further, ect. The point being that they have to had more and more reinforcement to the frame to have it be as robust as the BoF; from an enthusiast standpoint, that's just time and money and passion. From a manufacturer standpoint, that's a lot or research and development money and time into meeting a niche market; particularly when the majority want more "car-like handling" and less "truck-like robustness" that many of us on this forum expect from a 4Runner.
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Basically what I am saying is that to design a unibody to be as robust as a BoF, you'd end up putting more energy and effort to make it "truck-like" than it would be to simply go BoF; considering that the main goal of unibody is gaining that "car-like handling" it's sort of an either or issue, not really a compromise. A unibody out of the box does not typically stand up as well to repeated torsion and flexing forces that an out of the box BOF will; additionally it takes a lot of serious modification to get a unibody to be as robust as a BOF.