After studying the situation a bit more, I have concluded that the ARB 5421100 skids are not fully compatible with the early (2003/04) V8 4Runners because of the position of the crossover exhaust pipe below the transmission pan.
A friend of mine (2003 GX) has addressed this issue by using spacers toward the rear:
My concerns are that he is actually reducing his ground clearance and breakover angle in this way, he might get caught up on something if backing up, and the setup might not hold up if the vehicle actually comes down onto something (unless he upgrades to heavy-duty spacers and bolts).
Raising the crossover exhaust pipe even a tiny bit will get in the way of dropping the transmission pan for maintenance. Rerouting it would seem to be a major job that might open another can of worms, such as risking damage to the exhaust manifolds. I would definitely not consider that a simple bolt-on solution.
So, for the time being, I have kept the transmission skid off. I might ask the vendor and/or ARB if they are willing to buy it back from me...
I suspect that other skid plates might have the exact same issue simply because of the construction of these early models.