The other difference is the length of the USB 3.0 cable. The desktop version's is longer, since it has to reach under the desk, etc. I have both and I actually prefer the portable version for its smaller size and less noise. With the desktop version, it feels like my desk is humming a bit from the vibration, even two feet away from the drive. The speeds should be the same, I think. There may be other minute differences.
But the portable version's cable is really so short (looks like a bit less than 2 feet) that your drive will have to be very close to your computer case in order to work.
