...I haven't tried to build a core with a video card other than an nVidia so I don't know how far through the setup you would get....
My Core has a standard on-board GPU and I had no problems setting it up as such. Obviously you *could* have issues if you don't have the nVidia card but I wouldn't let that stop you from getting a machine if it is to be a core and not a hybrid- you can try it and if there are video problems get an entry level card that will work just to do the setup side.
Obviously if it's going to be a hybrid you need to think quite a bit more about the video.
The other stuff you may want to look at is environmental issues (I don't mean save the planet specifically, but where the box will be located). Are you going to hide it away in a server closet where noise won't bother anyone or is it going to sit next to your TV in the family room? Heat and airflow are an issue too. Also, depending how far you want to expand your system, you need to think of slots for cards (Graphics, TV tuner, Video capture etc), SATA ports for additional hard drives, things like that.