Yes we should expose that as a separate parameter.
We designed this to handle lighting your "whole house" and not just the lamp near a screen, so if you have a bunch of people living together, they usually don't want to have the lights change because one person disables f.lux :)
f.lux loads the current ICM profile, not any NVIDIA control panel settings. If you want to calibrate a display so all apps can use it, you should use something that makes an ICM file.