When it breaks they have to deal with it, not the f.lux team.
It's the same reason they don't want apps that ask you to throw your phone in the air, or put a bag full of sugar on the screen for weighing purposes.
Not justifying anything just explaining their PoV.
This is a bit of a strawman argument, F.lux is not in this category of silly apps. F.lux is a reasonable app it has a good track record respecting its users and is requested by many many users. It is about control.
Think about the cost to Apple's support teams after grandma is having problems with her phone being yellow. Her grandson definitely was not messing with her phone, at all...
Not justifying anything just explaining their PoV.