This is an exciting topic and I gave a great deal of thought at it before your post and I would add this question, why isn't there better technology?
At this point is my belief that the Zion faction is the only one that extracts red pills.
Gray and Flood comments when they contact you make me think they do not really have extraction facilities as such.
At this point, the question is if Zion is a free port and I think is safe to assume that Merovingian and Machine HvCFTs land regularly in Zion for refueling and operatives use as well the large broadcasting centers that were developed after the truce.
I think is not realistic to assume there are other cites because of the logistical barriers, the Zion that lasted the most in previous incarnation lasted 72 hours so the question at this point is, were they destroyed and beyond repair or Zion was rebuilt at the same location.
If option 1 is true, is fair to say that scavengers could build a life there with a bit of effort but nothing more that a Spartan outpost as the resources to build a proper city are really beyond the humans.
At this point, especially after the last confrontation at the end of Matrix Revolution, the damage sustained was massive and I am sure Zion is not recovered 100% yet.
Merovingian cities, because of the nature of the Faction I think they are unlikely; Machine cities with humans, possible but not effective in my opinion, machine are better off to have operatives in and out Zion... just in case the war starts again.
I guess another question is if Zion control actually knows which HvCFT belongs to which faction.
I think is unlikely and consequently, I think Zion is a free port and probably the only city.
Lastly, any RP reasoning can justify anything and outpost are certainly possible but logically I do not think at this stage cities exist, while maybe in 100 years or so things could be very different.
One interesting point is, if Zion is the only city and it is growing since the truce.
As they can use more resources to R&D and infrastructural growth, it is likely they are growing and improving now more than before as they are not in a constant survival/war mode.