Yes. After you are satisfied with the majority of the rods, you can enter edit mode for the meta-object and select each rod individually. Then use the settings in the properties shelf on the right side of the 3D view: View > Properties (N) > Transform. See blender’s metaball documentation.
No problemo. For really small, or really large meshes, the initial radius and polygon size settings may be off. So you might not see any metaballs until you fiddle with the numbers. Often the polygon size is too large; try setting it down around 0.50
This disappearing act can also happen when you rename the metaball object (by default it is 'MetaSkinned'). Just set it back to the default name and it should reappear. This seems to be a blender related error. I am currently trying to track it down.
Select "MetaSkinned" object > Alt C
Indeed, it is certainly behaving similar to a modifier. I even put the button in the modifier panel, because that seems like the most logical place. Unfortunately one can’t make blender add-ons into modifiers. Modifiers are written in C and would require a custom build of blender. Maybe someday metaball skinner will be a part of blender, but for now the add-on is a pretty good shortcut.
This can happen if you set the polygon size too small, and if there are many many edges in the mesh.
Also, if you have run the command a few times and have a few metaball collections, blender gets really fatigued. It is best to have only one skinned metaball object in a document at a time. Once you convert to a mesh it is fine to run the command again.
The default behavior of the metaball skin command creates a slight bulge at each vertex position. This is because the metaball rods overlap at the vertex. If you want to remove this you can select the MetaSkinned object (object mode) and go to Properties > Data > Threshold. Decrease the threshold to something very small like .0001. This will make the entire object 'sharper', with no bulges. As a nice side effect it will make the radius precisely equal to the setting.