I got two problems solved, the holes (B) and the position in the ebook (D). The solution is to replace the discontinued VRML function by the VRML tools included in the Simulink 3D Animation Toolbox. I got a license from the The MathWorks Book Program (very nice and supportive people) but getting started with it seemed to take some time, no easy and quick solution. Well, it seems that Stacey Gage did it for us almost a decade ago when he posted a recipe in the File Exchange:
It took a few minutes only to make Fig. 7.4 in my textbook "MATLAB Recipes for Earth Sciences" an interactive 3D graph. It really looks great now! Second, the newest versions of MeshLab and Google SketchUp make Blender unnessary, or is it the quality of the VRML/WRL file created with the Simulink 3D Animation Toolbox? The DAE files from MeshLab can be imported into Google Sketchup. Here I got problem (D) solved. You can easily change the proportions of the graph (scaling), the position of the graph in the axes (move) and moving the axes themselves (axes).