Filling basins on a selection as opposed to filling the whole map and then punching out the selection area is somewhat different, especially in terms of surface connectivity. The second process, for example, can result in large cliffs where a selection goes across a deep basin, for example.

Wilbur doesn't have a native file format as such. It has a load of formats that it can import or export. MDR is a very simple format with a header specifying width and height and the data stored in 32-bit floating-point values. The program may ask questions about encoding, but I assure you that I've never gotten around to implementing anything other than just a straight 32-bit FP raster. So exporting a file as MDR will let you load that file at a later date with exactly the same height information, but it won't save anything about the shaders to regenerate the viewed image.