OK, I must have misunderstood what you were asking about. The batch download tool allows you to draw a box around an area and have TopoFusion download maps from internet servers to your computer. It doesn't have anything to do with exporting maps to your GPS unit. That is only done within the "Export View" function, and functions as you've seen -- by exporting the current map view. It will download any missing tiles from internet servers to your computer as it goes.
Hope that helps!