Maybe. This seems needlessly deterministic, to me. I think work on other mechanics could make natural borders emerge as it were naturally:
- if non-accepted cultures actually meant something (e.g non accepted cultures should never lose separatism),
- if separatism meant that autonomy trends strongly upwards and has to be counterbalanced, and that peace treaties can include a demand that X culture or X religion be granted a chunk of autonomy,
- if autonomy trended toward an equilibrium instead of zero,
- if autonomy was affected by terrain (mountains are impossible to make not-at-all-autonomous in 1444–1821) and adjacency to autonomy was impactful (you might police your heartland real good but you can’t stop those damn brigands coming out of high-autonomy border areas to raid your rich lowlands),
- if the autonomy equilibrium point (and deterioration/increase) was affected by distance and distance was modified by terrain (Lhasa should count as further from Kathmandu than Comorin),
- if autonomy trending up was fairly normal and something you have to conscientiously resist by stationing troops and building forts in distant territories, so that maintaining distant, hostile-terrain territory has a significant cost and imposes a meaningful cost in wartime (trade control over my Iraqi fringe territories for victory in my war in Khwarazm?),
- if autonomy, once granted, is very hard to rescind (e.g 100% autonomy should be a daimyo-like vassal that can defend its autonomy and even independence by external diplomacy and force of arms)…
…if mechanical tweaks like that were implemented I think “natural borders” would swiftly become an actual (but not impossible to overcome) concern for many players. If the AI could be taught to understand that mountain, forest and river frontiers are more defensible than alternatives, it could understand the same thing. I don’t know that we need specific natural-border mechanics to achieve that goal.
Edit: similar considerations could be added to maintaining occupations. If occupying territory cost—as it does and always has—a significant fraction of the wealth and manpower that it took to capture that territory, total wars as we see in EUIV would go away entirely. We don’t need special mechanics to do that, we just need to make it untenable for the real-life reasons it was untenable: because you needed too many resources spread ever more thin to maintain control; because the people didn’t want to be occupied; because keeping control of difficult terrain is almost impossible, and so on.