I'm not here to put the blame, but to understand.
A third and a fourth pair of eyes would have helped a lot during flt preparation and the briefing on the SID. They could have spotted the very "wrong" 00000 in the MCP.
With only 2 in the cockpit, at 2 or 3 am as it was the case, a bit less easy...When you're on a flight with 3 or 4 pilots, if I'm relief, I sit in the middle, help my friends, and check too. You see many things from behind...
So, were they all in the cockpit?