Yes, VIN cut keys are really the only way to go, IMO. I just replaced all my keys with VIN cut Toyota key stock and I can lock/unlock every lock very smoothly. All I needed for the key code was title/registration and drivers license.
Just be sure that the dealer can vin cut older key codes. Here in the north Dallas area, Toyota of Plano didn't have the right equipment to cut from my key code, but Toyota of Richardson did. For about $30 I replaced all keys and they work perfectly:
90999-00163 - valet key
90999-00165 - master key, no protector
90999-00174 - master key, with protector