Based on further research, I suspect that this is impossible with OS X. Flux requires a digital signal to the monitor so it can control monitor color settings.
The Mac Pro has multiple digital DVI and USB ports. But the DVI ports all send the SAME image so they cannot be used concurrently to drive multiple screens with different images.
And the USB ports send only a data signal that lacks monitor control of things like color settings. So even if they're transformed and connected digitally, for example with HDMI, Flux doesn't control the monitor color.
One solution to this problem would be for Flux to optionally control colors by directly changing colors in screen buffers, but that would be a major engineering change.
Am I wrong?