This is just the picture, which float in my head, after knowing of tb3 news.
		
		
	 
   I doubt it.     TB v3 extremely likely still maxes out at  two ports per controller.   So six ports is still three TB controllers.   It doesn't buy anything at all to go up to  five controllers.   There barely enough PCIe bandwidth to support  
two TB v3 controllers, let alone more than double that amount.   If keep the dual GPUs ( highly likely)  there is not enough PCIe lane bandwidth to go around for five controllers.  Crank up the PCIe SSD to higher speeds and even less so.
   What going to end up with some sockets that only support USB 3 and some others that support multiple protocols ( the Type C alternative modes ).   Probably only the alternative ones goes   Type C.    The ones that only do USB 3 are much more a natural fit with Type A connector.   It goes just as fast for USB.  It is also far more backwards compatible with the billion or so  USB devices out there.
    Which port is "USB only" is also much more easily recognizable if use the two types to distinguish.   Maybe Apple will be so  OCD that want the super symmetry at the physical level while making users read a manual to figure out what goes where.  Perhaps overly optimistic they are not that cray-cray crazy. 
    If there are three (or more ) Type C connector pairs I'd expect something more like a  USB block on top consisting of 
   Type C     Type C
    ___usb logo ___
   Type A      Type A 
   Type A      Type A  
and a Thunderbolt block of  
    Type C    Type C
    ___ TB logo ___
    Type C    Type C
The top 6 USB only sockets are connected to the six USB 3.0 provisioned by the C610 chipset.  
The TB block would either be lacking USB 3.0 or just use a similar discrete controller that the current Mac Pro uses and optionally flow those through the TB flavored Type C ports.
  Physically separating the two flavors of Type C should help lower confusion.   If Apple wants control costs and lower confusion even more then  just  four Type A's an four Type C's  (and put 1-2  USB 3.0 hub(s) inside to expand the six from the chipset into eight. Probably feed the TB ones with the hub watered down bandwidth as those ports more likely used for   TB or DisplayPort  )
   The drop to just two pairs with TB controllers behind them works in most use cases  because the bandwidth doubled (and can still daisy chain). 40Gb/s and perhaps if GPUs are ready at that point  DisplayPort v1.3 in pass-through backward compatible mode.   The HDMI port goes to v2.0 and doesn't "share" a video source with a TB controller.   If need more than 5 monitors then need to use a monitor that can daisy chain either  DP v1.2 or TB v2 or 3.  Less than 5 monitors is probably vast majority of users.