23 November 2016
Doing mesh scanning at runtime is possible but not included out of the box. You will need to copy and modify the editor code that does the mesh scanning to allow it to work at runtime.
In more detail:
You will need to examine the code in Scrtipts/Editor/MeshScanner.cs and create a runtime version of that code by removing all the editor specific parts of it. Begin by copying the cs file and moving it out of the Editor folder and renaming the class. Then remove the using UnityEditor;, and you will see which parts of the code you will need to fix to make it runtime compatible.
For example, there's an Editor.Instantiate call in there to create a new PicaVoxel object that you would need to replace with a normal instantiate on a blank prefab of a PicaVoxel volume (which you will need to create). You will also need to remove the editor progress bar code as well. Possibly some other stuff, but this is off the top of my head as I don't have Unity in front of me at the moment.
To answer your second question: The mesh scanner should absolutely fill the inside of the mesh as well, but it will depend on the mesh. The scan does two passes: the first pass lays voxels on the mesh edges, the second pass does the fill.
If you're not getting filled meshes then there is probably something with the mesh that is causing the fill to fail. This might be flipped normals or perhaps too small or too complicated a mesh.