Hmmm... but that doesn't mean they didn't establish bases throughout the US, on their journey. This is the former US Government we're talking about here. They must've had a continguincy(sp?) plan, in case something like Navarro happened again.
The MWBoS control the area outside of Chicago, yes. and Fallout 2 tells us that the Enclave congregated on the Rig, which was then blown up, the survivors from Navarro, after losing more men in the battle where NCR took control of Navarro, they made a pilgrimage across the entire American Wasteland to DC, establishing bases along the way (Chicago outpost) but, given the circumstances, it is unlikely that any established outpost would be of considerable size, likely only refueling stations manned as minimally as possible so they can remain as unified as possible, after getting to DC and reorganizing under Eden, Raven Rock (Where i assume the civilian population of the Enclave was, on lower levels we had never seen) self-destructed, then a large number of soldiers get wiped out by the BoS and Optimus Prime in the battle for Project Purity and Autumn is killed, then they reassemble again under... nobody... and occupy Adams Air Force Base, when that plucky wonder from Vault 101 walks up and hands them their walking papers, delivered via orbital strike ballistic missiles, once again destroying another supposed "majority" of the Enclave for the third time in a row. The Enclave is [censored] dead, the only thing left are Remnants.