My point is that you are getting $20k of stuff that actually moves the car and the stuff in it from A to B and $10k of niceties (comparing base price to loaded price). I'd guess that people buying 4Runners are more for spending their money on stuff that adds capability than stuff that makes their bottom less likely to sweat. It is just a function of the priorities of the buyers.
Now, as to whether or not Toyota should offer all those things, more than likely their market research says that not enough people are willing to pay for it or those that will just jump to a GX460 instead. Without knowing what the production capacity is and how the 4Runner is produced from a development and manufacturing side, it is hard to say if the numbers flesh out that they should or should not add these features. That ultimately will only be known by the product planners at TMC. Development and manufacturing is such a complex web that the craziest little things can cause something to be offered or not offered. Sometimes it is the dealer groups screaming for it, sometimes it is a supplier that can only build X number of a certain part before they have to invest in additional capacity that blows that trim or feature out of the water from a unit cost perspective. Sometimes a car or trim is offered because there is a political incentive to do so (Mirai for example).
Having been in the automotive industry for 11 years now, most decisions aren't made because the planners are idiots. They do the best with the data and cost available to them to make a product that meets the market demand while still being profitable. Honestly speaking, I don't think TMC sees a future for the 4Runner. Regulation and buyer desires are increasingly at odds with what a body on frame, real 4WD SUV does well. Hence, we will likely see one last refresh of the 5th gen before the 4Runner goes away. They can build Highlanders and RX350s on Camry platforms to share cost. They can build Rav4s and CH-Rs on the Corolla platform. The basic structure of the car is the same and that gives those vehicles a huge leg up on having a solid business case. Ford has the production capacity to build 600k F series trucks a year, so they almost need everything from a regular cab short bed F150 to a Raptor and everything in between to fully utilize their factories.