Here is what I get when I go to the Model Maker module at step 5:

Model Maker standard output:

Adding 1 pixel padding around the image, shifting origin.
WARNING: output directory is an empty string...
Made models from labels: 1
Models saved to scene file slicer:06AF3520#vtkMRMLScalarVolumeNode2.mrml

If you ran this from Slicer3's GUI, use File->Import Scene... slicer:06AF3520#vtkMRMLScalarVolumeNode2.mrml to load your models.

ERROR: In ........\Slicer4\Base\QTCLI\vtkSlicerCLIModuleLogic.cxx, line 1593
vtkSlicerCLIModuleLogic (4F0E6A90): Model Maker standard error:

ERROR: no model scene defined! Using slicer:06AF3520#vtkMRMLScalarVolumeNode2.mrml
WARNING: If you started Model Maker from the Slicer3 GUI, the models will NOT be loaded automatically.
You must use File->Import Scene slicer:06AF3520#vtkMRMLScalarVolumeNode2.mrml to see your models (don't use Load or it will close your current scene).

Model scene file doesn't exist yet: slicer:06AF3520#vtkMRMLScalarVolumeNode2.mrml
Error: no model hierarchy node at ID "", creating one

The model maker crashes running from GUI when it is trying to
commit a scene with RootDirectory=NULL.
It happens in Applications/CLI/ModelMaker/ModelMaker.cxx line 1683.

As for hierarchy visibility, it's a separate issue, I am working on it.

Fixed displayable manager and CLI scene importer to display output of the model maker.
At revision: 18710

Dear issue reporter,

Good news :) Slicer developers SOLVED the problem you reported - YOU now need to VERIFY and CLOSE this issue.