As far as I know only Android >=7 on hardware with a HWC 2 implementation support colour transforms [0], so all Android apps implementing a f.lux-style thing do exactly that, draw an orange rectangle over the screen.

F.lux on desktop has always worked that way though, I think. It should essentially be rendering the blue component substantially darker (up to removing it, depending on the temperature setting), instead of alpha blending with orange.

[0] https://source.android.com/devices/tech/display/night-light....