I don't know for certain that it's impossible, but I must say that I have my doubts.
The reasoning is this: Even if a script modified the way that the Areas were handled, the editor would still only ever be able to define them as rectangles. Somebody out there who's better than I may find a way, but I feel that this is going to stack up a lot like the attempts to change the number of tilesets: even if scripters succeed, you still can't use them in the editor itself without hacking the thing, an endeavor this community doesn't support.
(Of course, it may be possible to build the script in such a way that naming conventions for the area rectangle tell it only to add its encounter list if you're standing on one specific tile, such as an Area box that would only have an effect if the party were standing on the second tile of the third row in the tileset (the default forest), which would be effective if it could be done, but I wouldn't even know where to start.)
