The working distance (in front of lens) is a major factor using macro lenses. At two inches, the lens hood surely has to be removed, and the lens probably still blocks the light. The longer focal length lens will be able to stand back a little further.
But that is really speaking only of extreme 1:1 closeups. To use the macro lens to copy documents, or for a typical tabletop scene, maybe the scene is only 12 or 18 inches wide. Then the 40mm or 60mm lens will be very conveniently placed maybe 2 or 3 feet from subject, where a 105mm lens (which may not scare bugs as much), may have to be back 7 feet (esp on a DX camera), which becomes inconvenient. On DX, 105 mm becomes an Effective 160mm telephoto view, so far back that we cannot reach both table and camera at once, and the room might not even be big enough to fit this in.
So there are always pros and cons of any choice.