How will the new Touch Bar & Touch ID work with Windows/Boot Camp
I actually had the same question as I want to use Boot Camp and the function buttons are now virtual and their answer was that yes Apple will provide a setting in Boot Camp to have the function buttons appear in the Touch Bar.
I'll provide the exact text from my chat:


  David: 
  Hey there, my name is David. Welcome to the Apple Online Store. I would be very happy to help you with your questions about the new MacBook Pro.
  
  David: 
  This product will definitely be capable of running in Boot Camp mode. May I ask, are you already using a device in this way now?
  
  Me: 
  I'm currently using a MacBook Pro for late 2010 and am running Windows 7 on it
  
  Me: 
  The reason of my questioning is due to the Touch Bar which makes the Function keys a virtual thing
  
  David: 
  Yes, they will be virtual, but there is a setting that allows you to show the function keys.
  
  David: 
  When in boot camp mode, you’d want to switch the touch bar to this setting, and they should function like normal.