So, I'm more interested in the gameplay mechanic, but as a historian of sorts, you're quite wrong in that there are many, many examples of cities or fortified areas being able to outlast invading armies and thereby stopping a superior military from taking land and resulting in a new "owner" of a country rather than just a temporary invasion.
Hannibal invaded Rome, won Cannae where nearly all 70,000 Romans died in battle... but he didn't have the manpower to take Rome, itself, even though it was mostly defenseless apart from walls and militia. He'd spend years in Roman Italy killing soliders but never got land as Romans wouldn't offer a peace deal, and Hannibal couldn't take big cities via siege. Conversely, the Roman engineering Corps made Roman invasions extremely successful against fortified cities or river networks of defense.
The Danish invasions of England over a century failed precisely because of a) city walls, and b) Alfred the Great eventually making as many cities as possible into Burghs, i.e. fortified walls. Danes and then other Norsemen would frequently plunder the countrysides but struggle against a Burgh system where the harvest could be protected and relatively untrained soldiers could withstand a siege against elite infantry.
The Byzantines held onto to Byzantium so long (even as the Byzantine 'empire' shrunk over centuries) precisely because its walls were so difficult to take, and its geographical location in the Bosphorous. Byzantium resisted all comers, even if armies routinely rolled into what is now Turkey and won battles.
Anyway, the impetus for a Capital city, or even a few "major" cities being untakeable unless the invading army learned siege techniques (Genghis and Alexander were famous precisely because of this ability to learn and adapt after a setback taking a city) is vast and I could give example after example.
As a CiV mechanic, it does make Tall and Turtling until Artillery (a ruthless siege-breaking device) entirely too comfortable a strategy. Hence my original query to open this thread: if Beach/Shrik want to reduce comfort zones, the artillery tech path/mechanic needs to be altered to make a player play differently than core-4 into Ideologies into Aborb nearest neighbor with Artillery. So long as you can pre-build cannon, artillery is vastly superior to an Air Force you need to hard build and came later in the path.