I don't think so, if you take the communications operator into account. (I can't link it ~due to strong language, but its easy to find).
The Operator talks with the Chosen until he gets suspicious, then runs a trace... and is shocked to find him on the mainland; "That can't be right", he says.
All information points to them having one major HQ, and a skeleton crew at their new base on the coast.
Yes I do remember that. But he says that in context of alerting internal security to the Chosen One's location. I think he was confused as to how a stranger was able to access PoseidoNet via a terminal that was not on the Oil Rig (seeing as there are only a few (4?) terminals that can still access the network at the time), not as to how a Enclave force would be on the mainland. There is evidence of Enclave bases in the west other than the Oil Rig, such as the Remnants Bunker in NV, which was originally a refueling station for Vertibirds. Also, remember that after the Oil Rig was destroyed, even though Eden ordered Autumn to move the contingent east, some decided to stay (I'm a bit foggy on where I got this, but I'm sure it's canon). It's possible that some Enclave forces relocated elsewhere and reactivated some military bases (most likely in the North if they did, since the NW was closest to Alaska, excluding Canada). With any luck, the Northern Passage might be used for an upcoming Enclave DLC (unlikely as it may be).
On a side note, if they do ever bring back the Enclave, Dornan needs to be in it, one way or another.