My understanding is that they will be completely different models/weapons for uniques although I may be expecting a little to much. FO3 really dropped the ball with unique weapons, honestly how unique can my weapon be if it looks exactly like the other Hunting Rifle or Assault Rifle in my inventory? :tops:
This is what has been confirmed: Uniques will all have unique skins, as well as stats that make them "better" than fully modded normal weapons of that type. They will not be modable.