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If there is, how will this be handled with the scale being what it is per hex ?

Some ground terrain is impassable over a certain hex, ex. Mt Everest. Of course planes can still fly over. Units will "Path" around these hexes, in fact they will always take terrain into account when determining best path.

As for how the map scale affects this, well we look at that on a case by case basis. In the World Map for instance, part of Mt Everest's hex will be passable making it not an impassable hex any longer. (Probably just a "Mountainous Hex")