Autumn grew up on oil rig. His father was a top scientist. It says in strat guide that Autumns father was ordered to take high-ranking officials to Raven Rock, because it was only Enclave location with a functioning ZAX computer.
From the wording of this, I would say the presidential order came from Richardson. This could have been a pre rig explosion order, or a in case of emergency order.
It doesn't really say when in timeline order was given.
It also demonstrates that there ARE other Enclave bases, but only Raven Rock has a functioning ZAX.
It also says he only ordered to take high-ranking officials. Doesn't mention an Enclave army, and nowhere in game does it say all Enclave forces came from Navarro. The only Enclave who would be in "retreat" are the government personel from the rig.
So, it is speculation where the actual troop faction of Enclave came from. While many may have come from Navarro, it is very possible other troops came from other bases, some of which may be more militarized than political or research based.
From in game dialog with Autumn it is clear there is a rift between political goals of Enclave and military goals. Autumn is miffed about FEV, stating that plan was abandoned months ago.
Most other Enclave activity is nothing more than pure speculation. This includes Chicago Enclave forces. However, seeing how Enclave remained hidden in DC for roughly 30 years+ when Autumns father went there, it would be safe to say they can remain hidden if neccessary.
Only actual facts about Chicago Enclave is that, it exists, there is more than one outpost, and they are alive at least around time frame of FONV seeing how Ed-E has Illinois license plate, which I would take as sign he made contact. Actual forces, mission, and where they came from, or if always there, is pure speculation.