That was also one of my early queries when adopted OS X Lion a little over 2 years ago. The article referred to is a good one; it applied all the way back to OS X Leopard.
The real question is: Why hasn't this been fixed before OS X Mavericks?!
Add to that the obnoxious (and identical) spate of permissions repairs which show up every time Disk Utility is run — pretty much the same list referenced in the article. One would think that the repairs should 'take', but they don't, if in fact they are 'real'.
Gee Grelber where were you back in the OS X Public Beta and OS X 10.0 when the "safe to ignore" repair permissions error/warning messages first started? From time to time they have disappeared, but generally only because Disk Utility or rather the underlying Unix command was coded not to report them (the messages were still generated, but Disk Utility simply didn't report them). I once read an article that purported to explain why new ones show up in each new iteration of OS X, but by that time I had long since learned to ignore them so I didn't pay enough attention to remember the explanation. I just figure that the sun will rise in the east each morning and new ignorable permissions warnings/errors/messages will appear with each update/upgrade of OS X. It is inevitable.
