Have you tried "dim on disable"? It may help.
Regarding your question:
The system in the eye that adapts to color (and brightness) takes several minutes to adjust fully.
So one case for this feature is if you are using Photoshop and quickly responding to some IM messages or emails that come in. And basically you want to stay adapted to the "brighter" condition and not roll back and forth.
In this case, it turns out flipping between settings very quickly is incredibly disconcerting...the early prototypes were so bad I held back for a couple years on shipping the feature at all. (I thought the slower transition helped a lot!)
There is no good solution in f.lux right now for changing between white pages and dark ones, but it is important I agree. We have had prototypes of this for years but they basically involve hitting the GPU pretty hard to figure out what the screen contents currently are....impacts battery and overall performance, etc. (There are ways to do this but they are not exposed by the OS.)