Currently, the flag is not touched. So for instance to All configuration and then back to WorkbenchRelease lets following flags
MITK_BUILD_ALL_APPS
MITK_BUILD_ALL_PLUGINS
MITK_BUILD_EXAMPLES
set to ON. So actually the WorkbenchRelease config works just for a clean superbuild.
Yes, switching configurations might leave some options ON which are not included by default in the newly activated configuration. This was a design choice.
Switching options to OFF when using a build configuration seems to be a dark path... every newly introduced options would potentially need to be forced to OFF in all configurations which don't set them to ON.
For me, this is a "known issue" with which we could live with so we don't over complicate things.
Reassigning to Stefan. IMHO, this is probably not worth the additional trouble / complexity.