I can tell you that I had the idea behind f.lux way before I even heard about the existence of f.lux. And if I did, then certainly somebody at Apple did as well.
The 'hard' work is implementing the concept (ie, writing the code), not figuring out how to change the colour temperature. Have you ever looked at the white balance slider in image editing? Night Shift and f.lux are doing nothing else then adding a WB slider to the graphics pipeline. And I might add display calibration software already let's you choose a colour temperature. If you wanted, you could have simply created to display profiles with differing white point and manually switched between them. What f.lux has done is merely automating that switch.
Apple buys out smaller companies if they have special technology (or talent). It doesn't buy them out if they just have an implementation of a general idea. And Apple is no different than any other company in this regard. Imagine a company that added copy and paste to iOS 1 & 2. Should Apple have bought that company when it added copy and paste to iOS with iOS 3?
And there is a general problem with Apple buying companies that offer software for multiple platforms. Can you imagine Apple continuing to offer f.lux for Windows and Android. There is only one single example where they have ever done this: Beats/Apple Music (which is available for Android) and that follows the trend that Apple has done with porting iTunes to Windows (ie, supporting their most important product, originally the iPod, then the iPhone on Windows). I am sure that you would have been even more upset if Apple had discontinued f.lux for Windows and Android after purchasing it.
Having key functionality of your application being incorporated into the OS is a professional hazard on any OS platform. Getting your panties into a bunch over it is like crying over spilt milk. There even is a term for it:
sherlocked (named after an application that searched the contents of your Mac which Apple made redundant by implementing Spotlight).
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F.lux is far from a perfect solution on the Mac. Highlights in videos are very often 'distorted' (blown out, show banding, I haven't bothered to figure out what is happening exactly but they definitely look weird and distracting).
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And what does Apple gain by rejecting such apps except for limiting the damage third-party apps could possibly do? Does Apple get more revenue by selling Night Shift as a paid add-on? Wouldn't Apple gain more money via its 30% cut if it allowed the app?