Why does my Mac Pro boot to black screen with third-party video card when holding Option key?
I don't know the precise technical reason, but unless your NVidia is specifically flashed for Mac it doesn't load the drivers until you reach the desktop. 

As you can see, this makes dealing with anything prior to that quite difficult. 

For boot camp the simplest workaround is to define the startup disk before rebooting. 

As you've noticed, keeping the old ATI for emergencies is a good idea.