No I don't see the problem, sorry.
I guess whatever internal conflicts which leads to "free cities" can be left up to the player's imagination anyway.
Technically, that is what Independent Cities (Rise and Fall) was meant to portray, but the mechanic is a bit under-developed IMHO. It's yet another area I hope they improve on and deepen in Civ7.
Yeah, I think there's some good potential here, even in dramatic ages mode. But where the game falls apart is that they don't explore the concepts, and it's too easy to "game" the system.
For example, if I am invading a civ, maybe the first city I capture from them you have loyalty troubles. But generally speaking, when you push in and capture their big capital city, that entire population immediately becomes loyal to you and pushes their loyalty on the neighboring cities. For me, most of my conquests is basically shuffling around governors until I capture enough of another civ that I stop caring about that anymore. IMO it needs to be a LOT longer after conquest that you gain loyalty. I mean, even a lot of internal conflicts in modern times are based on historical conquests. Quebec has "loyalty" problems in some respects because they were "captured" by the English 200 years ago. Similar with Catalan or Scottish independence movements, in many ways. I mean, obviously there's a million other factors, and it's not like Barcelona is breaking away to become a free city from the Spanish empire, but in civ terms, those are areas where you should need to perhaps have a governor stationed to prevent things.
Now, granted, everything in civ is abstractions, but I think some things to consider for the next version if they really want to represent this more:
-cities when captured should not be loyal to the new civ, and should continue to "fight" for their independence. If you wipe out a civ, you should need a governor stationed in their empire for like 50 turns after conquest to prevent rebellion.
-There should be perhaps more levels of rebellion and loyalty. Right now it's a little too much to basically be either 0% or 100%. Perhaps cities should be spawning partisans before fully flipping loyalty
-Larger empires should have penalties applied, and be forced to manage loyalty more. Again, not like "OMG my cities flip independent" every 40 turns, but like if war weariness gave even more negatives to loyalty as well as just happiness, maybe you should run into cases where if you stay in a long drawn-out war you really start having to manage problems both at home and abroad.
-It should also be harder to snowball era score. While I don't think it needs to be as strict as "after a golden age you should go into a dark age", the game rewards you too much for being ahead. Like my last game, once you start getting in the lead and conquering, it's just too easy to get more era score for wiping out civs, being the first to the next era, completing districts, etc... that most games I overshoot the era score needed by a ton. And then you get another golden age, with more bonuses, which makes you even more likely to continue and get more score, and get another golden age, etc... And since golden ages give you even further bonuses to loyalty, that also continues the cycle. If you make it exceedingly difficulty to chain too many golden ages together, I think that could at least simulate a little bit of internal conflict for civs that get a little too high and mighty
Again, I don't want my empire collapsing when you get too big, but I always feel too much of the trouble with civ is that I can have a big empire with an army that's spending 500 years wandering the globe wiping out everyone in existence, and everyone back home is busy building wonders, upgrading libraries, building sewer systems, and only barely needing to worry about the war. Like, even in Carl and Ed's stream, once Carl got his walls up, and had a few archers and swordsmen around that he felt safe, he was right back to trying to build wonders and infrastructure, despite his empire being at siege. Sure, at some point you should be able to turn back and continue growing, but in the game, especially once you have a little cushion, it's so easy to simply never worry again about your homeland, and be all too calm.