It seems inconsistent with where it was in the Legendary Ending? I thought he got in a pod that was on a wall with many other pods lined up against in but in Halo 4 he's in the back of a small room and there are only like 3 pods on this wall and there's one on his right unlike in LE. So, did Cortana move MC's pod when she was editing his armor? That's the only explanation I can think of.
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Is it annoying? yes. Just like redesigning the charon-class is very annoying. But it's hardly a major thing to complain about...