Map files are used to mark walls, hazards, ramps, and empty space within arenas. They don't work well for overlapping floors but they were designed to mark a multi-levelled surface. The only time that I'm aware of this data being used is when "Arenas.currentArena.IsStraightPathClear(XYZ-StartingLocation, XYZ-EndingLocation, IgnoreHazards)" is called. Which happens to be in most of the AI tactics ('Charge', 'Shove', 'Reorient', 'PushOffEdge', and 'Dethrone').
Arenas/__init__.py has methods for loading, saving, and creating map files but loading is the only one that works. It is possible to get the other two to work but it requires a bit of tweaking. Another option would be to use a text editor to make the map files by hand (it really isn't that hard to figure them out).