For anyone interested, on iCloud Photo Library beta:

Downloaded off device that image was taken with via Image Capture

  3942cf85f43282ece05ee01ef82f3b245e1638e6  IMG_2273.JPG

Downloaded via iCloud.com/photos

  0271267eb3fe02a27398e20e285cf14a26333510  IMG_2273.JPG

But probably the better test will be to see how files differ between iOS devices, and the Mac Photos.app when that is released.

...

Running this through exiftool, the image downloaded via icloud.com/photos has the following EXIF stripped which is the likely cause of the above change:

  GPS Latitude Ref          
  GPS Longitude Ref         
  GPS Altitude Ref          
  GPS Time Stamp            
  GPS Speed Ref             
  GPS Speed                 
  GPS Img Direction Ref     
  GPS Img Direction         
  GPS Dest Bearing Ref      
  GPS Dest Bearing          
  GPS Date Stamp            
  GPS Altitude  
  GPS Date/Time 
  GPS Latitude  
  GPS Longitude 
  GPS Position