There doesn't yet seem to be a way to ensure that the instance of ServerContainer returned from the ServerContainerProvider is the unique instance associated with the application where the call is made.
There have been a few suggestions as to how to do this, from using thread local, to adding the ServletContext as a parameter to the bootstrap call, to keying the instance by the context root. The latter two only work on web containers; this mechanism was also supposed to work elagantly for standalone containers.
We may leave this as a container specific mechanism for 1.0. We will gather more information from implementations before deciding whether this has to be addressed for version 1.0.