[Molly]

I use the Wilderness grid a bit myself, and my method is pretty simple. Each separate area that I attach to the grid, always gets connected either up or down, with the connection room flagged as Entrance. That way the main grid is always untouched and the maps work fine.
Since my grids usually are either space or ocean, the approach is natural; the 'special' areas being either planets or islands. In the few cases where I use the grids for other types of terrain, I use tricks like a walled in city on a cliff, to keep the special areas enclosed. You can of course also use portals that you enter, or climb/descend objects like trees and ladders.

Code is of course fascinating, but why make things any more complicated than they need to be?