The core graphics engine was new in each iteration of civ game. I don't know if there are many leftovers in other parts of the code, but providing modding tools are also totally new each time, I suppose each version of civilization is mostly clean new game, probably with some libraries reused.
AssignStartingPlots (always my go-to example because it's one of the areas I actually modded in this franchise) is pretty similar between V and VI, from memory. An absolute beast of a function, too.
I guess I assumed that despite the maturation of the pipelines, etc, that upgrades were always pieces, and the engine itself kept parts across each iteration. I swear there was a dev interview about this, back in the early VI days.
Choice is there, play as the Romans or one of the other 16/17 nations, play as the Romans and never build it
You don't have access to the other factions when you first play the game. Interesting lack of choice there, too.
Though I think at this point you've answered the question. No, you don't consider the Marian Reforms the same, because technically they eventually let you maybe opt out of it. Though notably, if you play a Roman faction, it's pretty hard (if not impossible) to not get to that point (especially as any other Roman faction can also trigger the Reforms).
I mean, there are plenty of other examples. Half of Portal is being told what to do, and there only being certain ways to solve certain puzzles (though Portal's ingenuity is in how this "feels" more organic, despite mechanically being pretty rigid in more than a few cases).
There are a lot of cases of a lot of games emphatically railroading player choice, even taking player agency away from them. These come with varying levels of popularity, success and / or failure (though nobody can really argue with Portal, in my opinion). Taking away control from the user is often seen as a good way to get people annoyed. Which is why the Age transition controls, with Legacy points, optional objectives to pursue that grant you additional Legacies based on how well you do, etc . . . all
give you control over how the transition actually impacts you.