When we tried the expansion last weekend, we realised the definition isn't quite clear in one case: is it possible to remove opponent's tokens from an area you share with him? Will your own tokens there also disappear if you do? 29.20 doesn't say clearly, and it isn't quite easy to extrapolate. (Depending on what side of the conflict people were, they saw it differently. )

Has this case been considered? A clarification in the rules would be good.

Reading §29.202 carefully reveals that it is possible to destroy shared areas, as long as no player with units in the area Fundamentalism or Philosophy. (Thus, if an area contains units belonging to two different player, of which only one holds Fundamentalism or Philosophy, that area can't be the target of Fundamentalism at all).
As the player using Fundamentalism obviously holds Fundamentalism, he can't use Fundamentalism on areas where he has units.

Is the following proposal for 2.08 any better?
29.201 During the Special Abilities Phase (25) a player holding Fundamentalism may destroy the occupants of any one area adjacent by a land border to an area containing his own units by removing all tokens and cities in that area.
29.202 The area may not be occupied by units belonging to any player who holds Fundamentalism or Philosophy (29.371). Barbarian tokens and pirate cities may not be destroyed by Fundamentalism.

We did read carefully. But the rules talks about units belonging to ANOTHER player, which could have excluded the player holding Fundamentalism. The section referring to OPPONENT'S tokens was also brought up in the discussion.

So yes, I think your modified is better. It is clear, and takes away those sections which could be interpreted as to allow clearing shared areas.

So all tokens are destroyed, but Barbarian tokens may not be destroyed. This means you cannot choose an area containing Barbarian tokens and tokens from an opponent who hasn't Fundamentalism?