Is there a quick explanation of why the f.lux can't simply be put into the App Store just like any other? Why did they have to try the "side-loading" method at all?
What f.lux does is (ab)use the CLUT to change the color temperature of the video signal sent to your monitor, cheaply and without requiring any modification to existing software. This is great if you trust f.lux, however clearly Apple cannot trust random apps with persistent access to the CLUT, because people could use it to do things like, say, completely blacken the screen.