If you have the new VR3186, you no longer have the same issue in crown position 2 as the old movement, as it is an entirely different movement. The old movement was not a clone of the rolex movement, as this new one is. There are still some minor issues that look like they need addressing, but nothing like the previous "3186" movement. I have never done hands on a GMT (but am now curious about this too), so I'll digress to someone more skilled than I. I would guess as long as the hands are all lined up at 12/24, everything should be ok when you go to reinstall them. If someone else would chime in and confirm this, I'd appreciate it.
Edit: I've watched some teardown videos on the tube- watchrepair channel does a teardown and service of the 3185, which is the movement your VR3186 is a clone of. It was mislabeled a 3186, but it's actually a 3185. Pretty much everything about the teardown of the Rolex 3185 should apply to this movement.