Regardless of Apple's claim that El Capitan automatically repairs permissions, I have found definitely one and possibly two incidents of the wrong permissions causing issues. The first was a UserEventAgent that was using 100% CPU usage until I tracked down two plists that had to be manually re-authenticated. And the second is my NvidiaDriverManager control panel which appears broken on my machine, which means CUDA won't run properly in supporting apps. So the question is, can I repair permissions on my El Capitan drive from Yosemite? After all these years I have never thought about if repairing permissions across OSX versions is safe to do.