I too do not understand the rational for Toyota's 5 tire rotation pattern. I have the OEM Bridgestone H/Ts, and Bridgestone recomends on their site a different 5 tire rotation. It is close to the Toyota pattern, except they recommend you cross the front tires when moving them to the rear, with the left front going to the spare position. This, IMHO, makes more sense, all five tires eventually get to all five positions on the vehicle. To me, this is the best method for equalizing tire wear between all tires as long as you don't have directional tires. Then a straight front to rear, rear to front is necessary. Of course, if you have directional tires, then you have to determine which side of the vehicle is correct for the spare, and include it in that sides rotation, if you want to use all five tires in your rotation plan.
IMHO, it makes more sense to include the spare in the mix. Why would you want to not make use of the spare? I have heard some argue that when it comes time to replace their tires, they only need to get three instead of five. But, when it comes time to buy new tires, how do you know the exact same tire will still be available so you have a matched set? With the spare in the mix, you should get about 20% more overall tire life on the set. And when it comes time to replace them, you may wnat an entirely different type of tire. Then what do you do with the 3-4 year old 'new' spare. Considering the constant advances in tire technology, it is quite likely that you will find a better tire in 3-4 years than what you have now. And even though it may not have been in use, the tire still has aged hanging under the back, do you want to trust it like you would new ones? And if you remove the spare everytime you rotate, you get to check its pressure, condition, and clean the debris off the wheel that tends to accumulate under there.