I noticed that when in Clamshell mode, Flux obeys the enabled preference setting of "Disable for full-screen apps", and so actually disables Flux while the MacBook cover is closed and the external display is in full-screen.
But really, and ideally, i'd rather Flux is disabled when both displays are active (MacBook and External Display, and not in Clamshell mode), and even better, disabled for either (or both) screen depending on which particular screen is in full-screen mode.
It's something to take note of.