I don't know if this will help, or even if my comment is related to your experience, but...
I have a 2002 Highlander and at around 60-65K kms, the brakes were feeling spongy. I think I had the original breakpads replaced at around 32K kms, and the dealership had noticed some irregular wear. At the next major service interval, I took it to my Toyota dealership where I bought the car, and had them inspect the brakes. They said that I'd have to replace all 4 rotors and pads. They ballparked the cost at approximately $800ish, but that was if they only replaced 2 rotors and machines the other 2.
My uncles a mechanic and I asked for his opinion, and we suggested that I replace all for rotors as well as the pads, and that the wear did look uneven in the rear wheels. The rotors had a significant amount of rust on them, and I felt it better to be safe than sorry. I had my break work done by him and myself, and for about $500 and change, I had replaced all 4 rotors with brand new ones as well as all the break pads. Of the original rotors, the one which showed the most wear had a groove on the back of it (seemed to me like a manufacturing flaw).
All in all, it cost me about $500, and I got all new rotors and breakpads and the knowledge that I can do it myself
