Another feature came to me after 3rd coffee.
User could specify contact constraints and boundary condition constraints over topological entities specified on particular meshes with the same name in Mesh tab. So, after importing all part versions, user would define topological entity with equal name for each part (mesh), and then in simulation tab, user would choose mesh of desired part version for simulation domain, and only reference this equally-named topological entity when setting up contacts and boundary conditions.
It would be forbidden to select two meshes with the same topological entity name in one simulation domain.
This way, user would not be required to re-specify contact and condition constraints each time he exchanges particular assembly part in his simulation domain. User would just exchange the part, and simply start another simulation run.