I agree with @m_baczewski. I have always thought this was odd behavior, and wandered if it was a bug or not. If we turn on one of the 'origin' WorkPlanes of an assembly occurrence from the main assembly, it also turns it on for all occurrences/instances of that same referenced model file. But if the WorkPlane we turn on is a custom one (not one of the component's 3 origin planes), then it will only turn on for that one occurrence/instance.
Maybe @MjDeck would know why this happens this way, and if there is a good reason for it, or if it is something that can be changed/fixed. After all, we are only working with 'proxies' of those WorkPlanes when doing this by code, not the 'original' WorkPlanes.
Example code:
Dim oPickedOcc As ComponentOccurrence = ThisApplication.CommandManager.Pick(SelectionFilterEnum.kAssemblyOccurrenceFilter, "Select a Component.")
If oPickedOcc Is Nothing Then Return
Dim oWP1 As WorkPlane = oPickedOcc.Definition.WorkPlanes.Item(4) 'or 1-3 for origin planes
Dim oWP1Proxy As WorkPlaneProxy = Nothing
oPickedOcc.CreateGeometryProxy(oWP1, oWP1Proxy)
oWP1Proxy.Visible = True 'or False to turn off
My suggestion in the mean time would be to create at least one custom DVR (DesignViewRepresentation) within that referenced model file, where that one WorkPlane is visible, and others are not visible. Then create any other DVR's (DesignViewRepresentations) you may want/need for similar situations, then save that referenced model file. Then, within the main assembly, set that one occurrence/instance to that custom DVR, while other occurrences/instances of that referenced model are set to other DVR's. This should lead you to the visual result you are trying to achieve.
Wesley Crihfield

(Not an Autodesk Employee)