I don't think Sardonicus is suggesting that Prime Base was purposely built to be a stalking horse, but rather that the changing technology climate made the original design less secure and as such its role was changed. Just like his example of Cheyenne Mountain where NORAD Command has been moved and Cheyenne Mountain was redesignated the NORAD Alternate Command. It is possible that the Prime Base we are discussing was redesignated as the Alternate MP Command and that a second location is the actual MP Command. Kind of like how the books say there are two bases.
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