From what I understand, Custom Shop models are much the same as the standard, widely available models, but there are a couple differences, like the finish, maybe the pickups, or the pickguard or something which sets them apart from those you ordinarily find.
For example you can get the LP Custom in only White or Ebony (excluding the Custom Plus), but I have seen LP Customs in Natural finishes, and they bear the Custom Shop stamp because of it. A G400 SG with a large pickguard is labelled a Custom Shop model, even though it is no different to a regular G400, apart from that pickguard.
In the Case of the SG Special Custom Shop, it looks to have different pickups, and that worn finish which isn't available on an ordinary Special.