I think you may be thinking that SubD face packing changes the topology of the SubD, it does not. It is instead a way of previewing and customizing how ToNURBS will create a Brep and where the surface seams will be. If you add creases to a SubD, this will alter the face packing as pack areas cannot travel across seams. If you add a crease and then remove a crease and want to reset the packing, PackSubDFaces can be used.
If you instead wanted to merge faces of a SubD, use MergeFaces or MergeCoplanarFace or MergeAllCoplanarFaces. I hope that helps explain it. In the future (past v7), we will likely offer more than one algorithm to control face packing too.
SetPerFaceColorByFacePack seems to be integral part of the PackSubDFaces command, but it is not explained in the PackSubDFaces documentation. There is a link to the PackSubDFaces documentation, but I am certain that most Rhino users ignore the link.
To do this you need the MergeCoplanarFaces command, the PackSubDFaces team doesn’t do that.
You can only use the SubDFacePack command to delete an existing face packaging and reset it to the default face packaging.