When working on WOH publish-configure and WOH retract-configure, several issues seem to be present in the current implementation (I haven't verified this, just looked at the code):
WOH publish-configure (with-published-elements == true)
Do not use the publications of channel 'internal'
WOH retract-configure (for publications published with with-published-elements == true)
The logic implements the with-published-elements == false case
For the true case, really just remove the publication element from the media package is enough (no need to retract files since they belong to other publication channels)
Documentation should better describe what the implications of using with-published-elements are.