So I went through this same thought process with my hemi grand cherokee. I was doing anything to improve the 12 mpg (yeah, the 4Runner really isn't that bad). The manual said to use only 87 or 89 octane, but I was getting 1-2 mpg better with 91.

The issue that was brought up about this on the jeep forums isn't that the manufacturer is trying to save you money on gas. As mentioned in other responses here, it's also about ecu tuning, combustion, designed temperatures, durability of materials (seals, metallurgy), fuel detergents, etc.. Even though it's also a vvt engine, but obviously different than the Toyota 4.0L, I stopped using 91, because I got some credible feedback on potential damage that can happen with continued use. Just something to think about - the engine isn't necessarily designed for 91 octane or higher despite performance improvements.