An idea: if you can't solve this problem, could it be possible to provide a switch to turn off Xinerama detection? Then Argyll will act as if there is only one screen. Using -p option, it is possible to place the color patchs on the right screen.
What I want is a way of detecting whether TwinView or MergeFB is running, to handle the situation more elegantly.
And as I said before, the common LUT for both screen is this is not a problem for me.
It may not be, but I'm not sure it's a good idea to fool people in general into believing that calibration is working for each screen, when in fact it is not. The conclusion to all this might be simply to say that "if you want to run color managed screens under X11, don't use TwinView or MergeFB".