In short, simple terms, the entire stack is one vessel. Each SRB, once "separated", is a vessel in its own right, with its own class. For the separation itself, the list of meshes which "builds" the Atlantis launch stack (SRBs, ET and Orbiter) is edited to uninclude SRB meshes, and two new SRB vessels are created in exactly the same place the SRB meshes used to be. The Shuttle vessel, now just an Orbiter and ET, is reconfigured to remove the SRB engines and adjust the mass accordingly, and the process is complete.
No attachment points required.
