I have an FSC Amilo Pi 2515 with Intel X3100 graphics card. The LVDS resoution is 1280x800. If I connect an external monitor/beamer which has a resolution of 1280x1024 and issue xrandr --output VGA --same-as LVDS to enable clone mode, my LVDS switches to 1280x1024 too. Yet I am unable to see lowest 224 pixels on my LVDS anymore and the screen doesn't scroll down with mouse on screen edge as I would expect from virtual resolution in X.
I use xorg-x11-7.3, xorg-server-1.4.2, mesa-7.0.3 and xf86-video-intel-2.3.2.
Sorry, that's not supported with RandR 1.2. It may be supported by the server at some point in the future.
randr 1.3 support is on server-1.6 branch now, so this should be tested against server-1.6 branch, and xf86-video-intel-2.6-branch.
If this is still an issue with current driver stack, please report again.