I've left mine alone from the factory (Locked in D, Unlock in P) but wish for the sake of my wife that they could code separate fobs for different driver setups so when she used it that it wouldn't unlock until Key-Out - and go back to the factory setting while I used it...But I ain't going to gripe about it, it isn't that big a deal to me. I also wish the window controls weren't in the door pocket either - wish they were on the console (or higher up in a different door panel design) - but ain't about to trade the 4Runner away over it.
But coding separate fobs for separate drivers is possible. My 2003 Chevy Traiblazer LTZ has it, and there are a lot of different settings between mine and my wife's "driver profiles" in its computer beyond the locking settings - and are activated depending on which fob locks or unlocks the truck. Our saved radio stations in that truck are even different depending on the fob used...Again though, you notice I bought a 4R and not another Trailblazer - so I ain't complaining loudly.