I can't see any reason that it wouldn't work.
However (there's always a however right?), I'd personally be a little leery of combining both ATI and Nvidia boards in the same machine. Seems like if you were going to use both, or for everything on the board to have the proper drivers up and running, you would have to have drivers for both ATI and Nvidia installed, rather than just one of them. I could be way off base here so get confirmation.
I would opt for either a Nvidia based mobo or a mobo without onboard video. That way you don't have video boards from both sides of the isle all trying to get along in one box.