How do they let this slip by but something of actual value like f.lux get's blocked...
f.lux was using private (i.e. reserved for Apple) APIs and was being distributed in an unapproved fashion.
FlexLight uses public (i.e. Approved for 3rd party apps) APIs and is distributed in the approved fashion.
Yes f.lux had a much smoother approach but that's because it was tapping in to parts of the system it wasn't allowed too. FlexLight made compromises in design to do it in an approved albeit clunkier fashion.
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Or, and here's a wild idea, don't leave your display turned on all night while you're asleep and not using it.
That's not what this is for. It's for using your phone before sleeping. Studies indicate that too much blue light close to bed time can make it difficult to fall asleep. People aren't keeping their phone display on all night.