The RCM absolutely are privy to some kind of revolutionary plans, the esprit the corps check during the ending is pretty unambigous with them making a list of officers that will "side with the people". It's possible that the Union plans to make a literally hostile takeover of the harbor is in fact another cover story told to you and that's just one step in "The Return", IMO seems like a plausible conclusion depending on how many connections the Claires have been making. Theres also a check that makes Klaasje talk about having heard of it approaching apparently.