SO.
Positioning/Rotating/Scaling at LOAD TIME should be done (IMHO) directly on the Geometry. So that no unnecessary time is spent on transforming the Shape at RENDERING TIME.
Some of these functionalities are already implemented in the GeometricMath class, it should be completed and methods added to the Model class.
Then we could even have an (XML-based) file format for models which specify the "real" model file (e.g. OBJ, Cal3D) and the modifications applied (e.g. scale, rotate, translate). Of course this file would be edited with a graphical editor (Xith3D+HUD) so that it'd be really easy to get your models right

Additionnally, this format could be extended with some JOODE-binding stuff (say, you have several XML files with a body, an arm, a hand and so on, you create another one to bind them all with a JOODE skeleton). But we're far from it.
And whoops Patheros already said that :
Third: For static transformations of objects (ones that apply to the model all the time) I think it would be more efficient to apply the transformation to each point before the model is constructed.
Last thing :
But you can use Amos' Transform class to do everything in one line (which internally creates three TranformGroups).
That's false. Now the Transform class is optimized and have only ONE Transform3D. It just multiplies matrices when needed (to add a Transformation to another).
Well, it depends the way you use it, of course, e.g. :
new Transform(node).setScale(scale).addTranslation(pos).addRotation(rot);
Will use only one Transform3D, whereas :
new Transform().setScale(scale).add(new Transform().setTranslation(pos)).add(new Transform().setRotation(rot));
will use three.