If your new frame is a Co-Motion, I am sure it needs no further preparation other than removal of the paint on the mating surfaces.

My experience mirrors rpenmanparker's. I have built up numerous frames over the years including multiple Treks, 3 Litespeeds, a Co-Motion and a couple of Surlys using cup-and-cone, square taper and Octalink cartridges and four external bearing Hollowtech II cranks and Cane Creek and FSA headsets. I have never had to face the bb shells or headtubes in any of these and bottom bracket and headset life and smoothness have all been great.