The dealer doesn't usually put those additional items on the vehicle...the distributor does (and the dealers themselves often have very little choice in the matter). All Toyota vehicles built in Japan are processed through regional distributors, and this is a holdback from the original days of Toyota's importing into the US. That system has remained in place even though in reality it just isn't necessary anymore. The regional distributors decide (sometimes with very little dealer input) what stock models to order and with what options. In addition, they will often add additional "upsell" items to vehicles as "port options". Dealers may request port options on incoming vehicles or delete them at will, but this is often only done for vehicles ordered though the distributor for special purposes (i.e., the customer "special order").
The limited availability of V8 engines is due to a number of factors including the new Tundra release making a good number of them allocated for that vehicle. In addition, the 4Runner has historically had a fairly small V8 "buy in" -- customers tend to opt for the V6 by a very large percentage margin. The performance difference between the two engines in this vehicle is one of the smaller spreads that is seen on this type and many customers do not perceive a huge difference between the two (and in fact for the most part and for most people, there isn't).
Vehicles are NEVER shipped back to Japan. Ever. It isn't cost-effective for any purpose. Problem vehicles are repaired in port or in a worst-case scenario they can actually be scrapped. I suspect your dealer's allocation isn't sufficient to get the vehicle you want right now so he is stringing you along until he can.
