Everything I've read at this group indicates that you shouldn't do that because of the possibility of metal chips getting inside the flywheel and eventually destroying the rubber inside the flywheel. I have just recently talked to a series of Toyota and performance shops on this and also to get quotes. Interestingly, the Toyo shops (2) didn't even mention replacing the flywheel, and said if its not warped or its does not have hot spots then they lightly resurface them. When I went to the performance shop Jotech they said when the replace the clutch they relace the flywheel. So I also would like to know which is the proper procedure. I would figure ... especially in my case with the car being nearly 7 years old at 100k+ you would change the flywheel. I also ask them whether it was standard procedure "while you in there" to replace rear engine seal and tranny seals. Here again I also got conflicting answers.
Ron