BUG: Restore original behavior of vtkMRMLNode reference functions

This commit continues what has been started in r23395, it basically reverts
the logic handling reference to the implementation existing prior to r23192.

It reverts all the changes (r23192, r23196) that were done to be
able to set/get a reference at a position N. But it keeps:

• the readability improvements to complete successfully. (r23193)
• the transition to smart pointer simplifying the code (r23191)
• changes done as part of r23192 and this commit fixing the
  following tests:
  • py_AtlasTests
  • py_CompareVolumes
  • py_SlicerMRBTest
  • py_RSNAVisTutorial
  • py_VolumeRenderingSceneClose
  • py_Slicer4Minute

It fixes "py_SubjectHierarchyGenericSelfTest" crash that is reported in
issue 0003754 and was "related to MRML references. There are still one more
problem that is most likely related to the way SubjectHierarchySceneModel
deals with QModelIndex. See [1]

[1] https://www.assembla.com/spaces/slicerrt/tickets/598#/activity/ticket:

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23414 3bd1e089-480b-0410-8dfb-8563597acbee