My understanding is that the SCR implementation bundle uses its own bundle context to track bundles that contain service components. A majority of the time this is the correct thing to do.
In environments that use an isolation engine there may be scenarios where the SCR bundle context does not have visibility to all the bundles it should be extending. For example, OSGi Subsystems or Equinox regions. In such scenarios it may be desirable to install a single implementation of SCR which has the ability to extend all bundles installed in the framework regardless of what subsystem or region the extendee bundle is installed.
One way to accomplish this is to use the system bundle context to track bundle to extend. SCR still needs to use the extendee context in order interact with the service registry on behalf of the extendee bundle (e.g. listen for service registrations, get services etc.).
If we do this there should probably be an option to enable using the system.bundle context and the default behavior is to still use the context of the SCR bundle