The Central Regime headquarters weren't intended to be visited since Belthasar wouldn't be so keen on letting the party wander around. Well, details about that part of the game were kinda sketchy in any case. But looking back, I think it's definitely good if the party does visit them before going to the rebel base (anonymously, without alerting the leaders). This would allow to better explain the political situation rather than have Belthasar and computers in Chronopolis dump all the details CC-Ghost-Children style.
I believe one of the daunting, typical aspects of the Central Regime is how we never really see its leaders directly (whether in CC or in all previous CE plot drafts), so I guess this location will be a base of the Central Regime rather than the capital.