I don't know if anyone is doing custom tunes on the 4-Runners (especially such a new model), but that is definitely the way to go. A custom tune will give you the most performance for the money. The canned chips tend to cost more and aren't as effective, since they're designed to be a "catch-all" tune for any vehicle.
And yes, it's worth doing, even on a stock engine. I've owned/driven a few tuned trucks, and love them. A custom tune will be the first mod to every vehicle I own from now on. It improves drive-ability, mileage and can be tailored specifically to your driving needs. You don't need a bunch of mods to see a big change in drive-ability, they can do a lot with just tweaking a factory engine.
As far as warranty, there's nothing to worry about. You can't just void an entire car warranty for modifications anymore, laws have been passed preventing that. Unless they can prove that your modification was the cause of the specific failure, they can't deny your warranty claim. They may try to pin some issues on the modified computer (like a transmission failure because the shift points have been changed), but even that's unlikely. A tune isn't going to cause any damage to the vehicle and they'll have no leg to stand on when it comes to warranty work.