Yeah, I read that report at Unsanity early on in my use of OS X. Figured since he was a dev, pretty well respected, he must know what he's talking about. So, I didn't suggest it for the longest time after that.
True enough according to what he says there may be some underlying thing that caused the permissions to be wacky to begin with and it probably would be best to fix that underlying issue.
That'd be great if there were a whole bunch of us that knew the underlying OS a lot better than we do, could read all those console logs and really understand what in the world we were looking at. Truth is, I don't (well, maybe a little bit now), and my guess is, the vast majority of us pleeb users don't understand those logs either.
After a couple of years hanging around forums and seeing the results of Repair Permissions being run as the result of others suggesting it and the strangest problems you can imagine disappearing afterwards time and time again, well...
Most folks don't care why their machine isn't working. They just want it fixed so they can get back to doing what it was they were doing.
I'm sure he was right, the suggestion to Repair Permissions is probably made a whole lot of times when it's not going to do a thing to fix the issue. But, it's too easy and only takes a couple of minutes. Read a few thousand posts over the course of 2-3 years and you start seeing how often it does work. For myself, it's worthy of being towards the top of the list - not the last resort.
Maybe if I understood the OS better, could read the logs and figure out underlying problems based on those a lot faster. In the meanwhile...