The problem is that you can make either unique custom tiles or generic upgradeable settlements. Because of that, you can not have a unique settlement which defences (and size) are upgradeable. It's one or the other.
To use DotS as an example: you can make Constantinople a unique settlement since it's defences did not change that much during the late Middle Ages, but places like London or Paris did change a lot (so they have to use generic settlement upgrades).
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