Doesn't the upgrade step(s) from v3 to v4 satisfy your requirements ?

There are no carving out/injection of project areas from either the back-end database or the repository itself.  It is all or none to be upgraded.   And aside from the database, an upgrade should always be done into a "clean install" i.e. a freshly installed CLM package including the needed JTS and/or applications.

There are also dependencies amongst JTS and its applications that must be met.  JTS must be "highest" ( at most 1 major version above its registered applications ) and if applications are co-located in the same J2EE provider ( i.e. installed in same WebSphere or Tomcat ) they must all be upgraded in the same "session".