Apart gqview, KDE is also able to work in MergedFB, like it does in real Xinerama mode. It sees the screen as one big screen (2880x1200 = 1600x1200+1280x960), but is able to restrict windows on one screen when maximized.
Right, but they are using the fake Xinerama information to work correctly, and don't have to access the underlying screen functions such as Video LUT access, like Argyll does.
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 will do is to benignly ignore the X error triggered when listing the available displays due to TwinView/MergeFB not supporting the XFree86-VidModeExtension properly for multiple screens, and this should allow loading up Video LUT values for the first screen, as well as it is a little difficult for me to verify that it works correctly). It should only error then if an attempt to load Video LUT values is made on the second screen.