I just started a new thread that deals with one of the issues you highlighted. My rMBP also is automatically adjusting brightness on its own even though the auto brightness box is unchecked. Candidly, it's good to see this is not only happening to me b/c maybe it's something inherent in the system and people just aren't noticing it?
To close out my original post, I never did managed to solve my flickering problem. I did every trick in the book, including SMC resetting PRAM etc. So, just as I had given up trying to fix, low and behold, my left side of the
screen one fine morning became rather dim. I knew that something , like backlight had gone on it. So, I still had
lots of warranty, brought it in. This time, because of it being a rather obvious defect upon looking at my screen.
The genius ordered a new LCD and backlight .
So far, no flickering, however, I still have the brightness level that drops down from a full brightness, no matter if I check off "automatically adjust brightness" or not. This being in a relatively dark environment.
I can imagine that there are many people still with this problem, with no obvious solutions that are 100 % effective.