I have played several games recently using the excelllent tectonics map script from the new patch.
It's a great map isn't it? It almost feels like it was included by Fireaxis as a challenge for us here to improve the AI. The choke points and terrain structures are a wonderful testbed for building a truly clever intelligence (SIDE NOTE: from looking at the placement of bonuses it looks like the map script has been adjusted for better late game corporate balance *I think*)
In your example, it seems sad that the AI only built that fortress for the stone and not because of it's choke point promise...
You'd think there would be a fairly achievable way of getting the AI to understand choke points but it probably is not simple in reality. As a quick pass you could do this to implement something short term:
1) Once x number of border cities have been established to y-culture execute 2)
2) If not at war with no threat of war execute 3)
3) Discover the extent of "terrain holes" on my now well established borders
4) If terrain holes are few enough execute 5)
5) Decide how to plug the terrain holes (forts verses units verses treat hole with the same defense priority as a city)
6) Plug them quickly....
Without a strategic planning AI, once 6) has been executed the AI simply returns to generic behaviour but keeps a track of the "holes" and refills them as necessary throughout it's remaining existence whenever it is not at war. It will of course do potentially stupid and unneccessary things like "overdefend it's interior cities" but at least it covers for the possibility of invasion despite terrain security. The algorithm beyond step (2) above is only calculated once for every "unique" body of culture the AI possesses or if the body of culture has expanded by a certain amount where upon the algorithm is re-executed beyond step (2). The complexity of this algorithm is probably on the same par as "amphibious invasion" if not more.
As for terrain funnels, that is too much of a challenge for this existing AI I think. However all is not lost because perhaps terrain funnels produce interesting "generic" behaviour in the AI anyway.
This is unsatisfactory of course, but without strategic planning what does an AI do? In theory if it could plug all the holes and choke points, it could concentrate military at these points and areas then underdefend it's cities and concentrate on it's economy...
Cheers.