Actually it was Enclave outposts in Chicago, not a full on base.Well there is a enclave base in Chicago(my hometown) iirc. I wouldn't mind seeing the last enclave chapter in existence try desperately to survive, it could make for a interesting plot, if it was handled with care. But Bethesda wil probably make the next fallout so it will probably be just more armored dudes to shoot at.
Also, that information was terribly out of date given that they act like Navarro was still standing, when it had fallen some time before.
Given that ED-E was repaired by some wastelander idiots, and not the Enclave, and given that Chicago is home to the MWBoS, there is a 99% chance the MWBoS already wiped them out, and took all thier stuff.
But Bethesda doesn't seem to have any itnrest in going into the Midwest, like how they have no interest in going to the west and "gave" Obsidian free reign to do whatever they wanted with the western US in New Vegas.