I would argue that any organization which has an important job and doesn't plan for the loss of its leadership during a nuclear war is incompetent. All it was going to take was one stray nuke and Prime Base gets obliterated without warning.
The whole 5 years vs 150 years makes the core job of the Project harder, but the lack of basic leadership made the whole thing a roll of the dice. The whole point of spreading the Project so thin was because of the possibility of losing individual facilities, they had to consider the possibility that the facility they would lose would be Prime Base!
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