In case anyone is still interested:
I've had the same problem. The nvidia internal xinerama gets deactivated if you use the server wide xinerama extension.
Basically all what xinerama aware programs (like kde) care about for their screen alignment is the reply of the XineramaQueryScreens procedure of the xinerama extension.
So what I've done is to fake the reply in the xinerama extension to match my real monitor layout - and indeed this works quite well :-).
I'm currently working on making this a config option, but if you'd like to have a preliminary patch with hard coded values, drop me a private note.