Except when it is transitioning color temperatures, I don't see why this would be the case. I reversed f.lux and it just calls some UpdateRGBLUT type function based on the color temperature. I think this LUT is applied to the frame buffer (perhaps this is how color profiles work?) even if f.lux is not being used.
First, f.lux periodically adjusts the LUT, so it does call this fairly often. Secondly, in my experience, adding this functionality seriously increases the odds that my laptop will switch from using the Intel GPU to the Nvidia GPU.