[pbh101]

By its nature, the functionality of their app breaks the app sandbox, currently via unsupported APIs. It is unclear whether Apple wants to ever support the functionality required to make f.lux run. My guess would be no, because it would be difficult/impossible to design without also allowing malicious behavior, and Apple is understandably keen to keep the App Store's reputation as a trusted and harm-free source of software.

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.