Sorry Phil but I'm still a little bit confused :-) Do you mind walking me through stage by stage what you would like as a player to be able to do. You've booted the game with only a keyboard connected. You then plug in a x360 controller. The x360 controller becomes the 'active' control method for you as the player. Are you saying you'd like to be able to control the character using both the keyboard and the x360 at the same time? So pushing jump on the controller OR pushing jump on the keyboard will both have the same result?
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See if this helps - when I plug a 360 controller in, the game will automatically detect the controller. Having the ability to recognize a controller is not a problem in itself. But, if there were a "keyboard-only mode," the game would not recognize a 360 controller once it's plugged in. However, even in this "keyboard-only mode" there would still be a way to use the 360 controller, because I could use a mapping program (like JoyToKey) to convert 360 controller buttons to keyboard commands.
I know some people love the fact that games can automatically map an entire 360 layout, but for me, there's a major loss of choice involved. In my case, other USB-based controllers (like an N64 or Logitech) are actually more attractive for use with this game, because the game won't recognize them as controllers, and because it won't, it also won't force a controller layout.