Repoulating an entire army would of course take longer, but in the time between 2 and whenever 4 takes place, they could have easily built their numbers up enough to be a faction in FO4.
I agree with you, but, we have no idea if chicago existed prior to rig explosion, was manned by Navarro troops, or what.
All we know is it exists. Troops, strength, who formed it, all a big guess. Likewise, existence of other bases is pure guess. Which is why I hope they are in FO4 so we can start eliminating guess work and replace it with actual lore. If they are 5 troops or 500, pre-existed or from Navarro, other bases or is this last stand, whatever, I would like to know.