I just confirmed that at least on 360 it gives you one of the defaults if you select custom appearance, it does NOT let you customize your imported face.
Could be different on PC.
*Edit* - I was able to get a face code on ME2 though by going to custom appearance, then backing out and selecting my imported shep. This is the method that the forum says will give you the face code for the new custom shepard though, not the imported one, so I'm going into ME3 to test.
*Edit 2* - Yeah, it just gave me the face code for the new custom Shep.