Cliveh, Bob is not clouding the water. He's saying he focuses wide open and then closes down two stops to make the exposure.
It depends on the lens. Most modern high quality enlarging lenses from Nikon, Rodenstock and Schneider should be free of focus shifting. Stopping down a stop (usually recommended for highly corrected top line lenses) or two, is really only to help minimize aberrations and falloff. It also slightly increases depth of focus (at the film plane) and depth of field (at the paper plane) which can help reduce the effects of incorrect focus, enlarger misalignment, and lack of negative flatness (assuming you don't use a glass carrier).
With older and/or lower quality lenses there can indeed be focus shifts when stopping down. You can sometimes see this in the grain focuser.
Try this: Focus wide open. Then stop down to the working aperture. Make slight/fine adjustments to focus and see if you can get the grain any sharper than it was. Once it is as good as you can get it, open up to maximum aperture again and check the grain focuser. You may or may not see fuzzier grain than when you originally focused wide open.
Perhaps you don't understand my point, as I am all for stopping down to print, but not to focus.