Not really sure what you mean by conformer.  To me it seems like the graft is merged into the main geometry of the G3 mesh.  The geometry is welded.  There are no hidden verts in the actual geometry of the new G3F or G3M mesh.  I don't edit the Graft in say DsonEdit and remove the graft portion of the file.  the only thing I do is convert the rigging to Blended which is needed for it to bend properly.  The Geometry editor takes two separate objects and makes one.  Am I making sense?  There is no conforming or "Fit to" operation that needs to be done after the two items are merged.