Glad I was helpful. Having spent the last 4.5 years using nothing but poly tools for game development, I've gotten to know polys pretty well.
Anyway, when you use a boolean, the output shape will inherit the normals from the input. For instance, say you want to use a sphere to carve a chunk out of a cube. The default poly sphere is created as a faceted shape. When you apply the boolean, you will get facets in the cube. If you average the normals on the sphere before you apply the boolean, then you'll get smooth shaded faces in the cube.
This is just the way it is with polys. You have explicit control over where each poly component goes, but you also have to deal with how the normals are calculated for the components. There really isn't any way around this.