Ask around at different dealers in the area.
I've heard of dealers who contract with local 4wd shops to install lifts, ARB compressors and lockers, aftermarket wheels and tires, skids, etc but bill for it on the dealer invoice.
If you get a double cab long bed, it sure would be nice to get an ARB locker installed in the rear if you plan on any serious 4wheeling. Upsize the compressor to the next largest model, and get the tire inflator kit & you have onboard air (the smaller ARB compressor only runs the locker). If you can, add a true 3-inch lift (not just spacers!!!) ... though this will affect gas mileage. If you do a lift, you can upsize tires too.
But if the dealer won't allow any of this, then I'd get the OEM roof rack (if you would have a need) & a nice shell (all dealers I've seen do shells), and new wheels and more aggressive tires (BFG A/T KOs are good for both on and off road ... lots of guys love the Goodyear Duratracs too).
Finally negotiate a 7yr/100k mile extended warranty. They'll try to charge you $3000 for this. Tell them there is a dealer in Massachusetts (Troy Dietrich - Toyota of Greenfield - dealer #20134 - 413-772-0231) who will sell the 7yr/100k $0 deductible for $950.00. When I told my dealer this, he offered to match the price because he still gets a kickback from Toyota even for selling it at cost (which is what Troy does).
Good luck .. and lucky you.