Dreamflower, I think the advantage to the .map tool approach is that you can turn the .map file into directx. Then you can use programs like 3d Studio Max to further edit objects in place. This is a feature that people have been asking for since CS2 came out.
There is also the possibility of using a "real" BSP tool for .map creation and then porting the finished .map file into cshop for light mapping and then putting the resulting product into a commercial product that can't be traced to the "real" bsp tools. (I haven't checked to see if the data is striped of identity.)
Take Care,
Ben