If you want a definitive answer, call Powercommander. That said, I certainly see nothing on their site to indicate it won't work, and they even list the stock ECU as part of their delivered map settings.
http://www.powercommander.com/powercommander/powercommander_iii_usb.aspx?mk=5&mdl=183&yr=2008
http://www.powercommander.com/powercommander/powercommander_iii_usb.aspx?mk=5&mdl=183&yr=2008