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?
In addition, I imagine other app developers might not be happy with a sanctioned means to mess with the running of their app: more interactions means more to test and less control over the user experience.
More likely is that this functionality will be incorporated into iOS itself in a future update. But it still runs the risk of Apple considering it aesthetically distastefuland thus never doing it.