Sure, it uses private APIs, but thousands of popular projects on Github (like game simulators) or that Apple TV web browser project all use private APIs and they are just fine.
The issue is F.lux for iOS is not a true open source download. It is a pre-compiled IPA file packed within Xcode to utilize Apple’s new free signing policy.
And to making things worse, the same F.lux Xcode project does not only allow side loading F.lux itself, but also any unsigned IPA file. This allows pirates to install any cracked app, without the need to buy a developer certificate. I have tested and believe this is the true reason for F.lux project being pulled.
Apple gets a lot of criticism over their decision-making & “closed ecosystem”. But you rarely ever hear people talk about how obsessed Apple is with the privacy and security of their users. In fact, you’d be hard pressed to find a tech company of Apple’s scale that does more for user privacy and security that Apple.