If you compare the GDC trailer and the game itself nothing has been changed in the scenes in terms of injuries on Snake's model and his dry sneaking suit. Only that missing scene has them, and there's nothing to really connect in either version except for after the bomb has gone off.
I don't think this was cut, I think we'll see this in the Phantom Pain's opening. As to why it wouldn't have been included in Ground Zeroes when it's 1975, this is just a theory but it's been confirmed that Kyle Cooper is back for this game who did the title sequence for Se7en and MGS2 & 3.
In some tv shows and movies they have what is called a cold open, it's usually something that happened before the real story begins and it ends with something dramatic (in this case, Snake blacking out and falling into his coma) just before the title sequence. Then after the title sequence, it would follow on 9 years later with him waking from the coma. They did something similar when they ended the Virtuous Mission with the nuke going off before the Snake Eater opening played, but in this case Ground Zeroes isn't seamlessly integrated into The Phantom Pain so maybe they needed to cut to black early for that reason.
If I'm right I don't know how Kojima will explain the chopper being in one piece after that cliffhanger, but then it is Kojima. Nanomachines, son.