This is gotten around on most of the missions in Beyond Good and Evil by listing two similar locations (Summit of the Father or Fairy woods for instance), you could easily create a list of alternatives to balance this out somewhat if it was a problem for you.
However, one mission in Beyond Good and Evil lists only one Location (The mission to fight at Maisen), if this mission is considered balanced against the others if all areas are included I don't really see how the missions from the original game would be less balanced than before.
If you did use the missions from the base game as written the biggest problem would be a greater favouritism of the old locations, because only 1 mission out of 20 needs the new areas, but 10 out of 20 require the old areas. This could be solved by disallowing the new missions to utilise the old areas. (Making it 10/10 old/new).
If you didn't want that limitation because the luck is too great, you could take the time to develop alternatives from the new locations for the old missions (and then it would be more like 18 for both; with I think just the Maleketh and Maisen missions needing a set location).
I haven't tried this yet myself but I intend too after a few more games. (The game is fairly new to me), when I try it (utlising the new missions can't use old locations varraint first) I'll post how it worked out.
If you're worried about the final missons, to balance them is the same deal, you need to either limit the new missions to new only areas or modifiy the old missons to include a new area s well. Personally I think in the case of the final missons, you need to make the old missons more flexible to prevent (probably rare) issues in crisis mode where it's just impossible to get the mission started.