I work for the company that makes both filters. The -38051 is made at a plant in Japan and the -YZZ13 is made in the U.S.
They both have the same design - the only difference is the pre-filter. The -38051 will hold more dust. The pre-filter is primarily for vehicles used in the mid-east (Saudi Arabia, etc.). So Toyota ships all vehicles with the -YZZ13. The pre-filter is not needed in the U.S. unless you do a lot of desert driving. And, you would have to do a lot of desert driving to actually need it.
Some dealers apparently choose to only carry the -YZZ13 version, but it is available online. I can't speak for why some dealers don't carry both versions. The -YZZ13 usually has a smaller price tag since it's missing the pre-filter.
The pre-filter is white when it ships in a new vehicle and turns dark after use. There is no charcoal in the pre-filter.
But the 4Runners come with the 38051. Probably because they are built in Japan. The Tacomas and other North American Toyotas may come without the pre-filters.
Many of the Audis, VWs and BMWs i've owned come with the pre-filters as well.
I was quite surprised, i just changed my air filter at 20k miles (over 15k with the more open TRD airbox installed). I live in a dusty, sandy area and i have around 750 miles of off-road/dirt road, etc driving. The air filter wasn't very dirty at all. There was some sand in the bottom of the box, but good otherwise. The TRD airbox lid has the filter minder installed, it never showed any restriction. Next time i'll probably run it longer than 20k.
The cabin air filter on the other hand...