Having only one global obstacle map is a serious limitation, and given the way they are actually configurable in the editor, this is a bug.
It avoids to have ground and air units for instance.
It avoids to have obstacles traversable by only one kind of units (private gates).
...
A pathfinding behavior shoud be connected to a given obstacle map, that can be shared with some other pathfinding behaviors for performance.
nimos100 mentioned to use layers to store these obstacle maps which may be a good idea.
Ashley, do you plan to fix this?