Not Just a Toyota Problem
I did some web searching and found that owners of Subaru, Nissan, and I think it was Honda products report the same problem: their factory service manuals say the slide pin with the rubber bushing belongs in one position and the reality of their vehicles is just the opposite. I'm guessing there must be one dominant supplier of brake calipers to the Japanese manufacturers and somewhere along the line they changed the location of the pin with the bushing on it and the service manuals didn't catch the change for a while. I still have no idea what the function of the bushing is. Just another one of life's little mysteries....