bbbezard It makes sens in older Blender versions (see my following post) to use a separate mesh in order to create a "Shapekey" from a "Bone Deformed Mesh" since "New Shape from Mix" creates a "Shapekey" only from the deformations caused by all currently visible "Shapekeys" together and doesn't take deformations into account which are caused by "Deformations Bones". "Shapekey Deformations" using only one mesh are created exclusively in "Edit Mode" whereas "Bone Deformed Meshes" are created in "Pose Mode". "Join as Shapes" on the other hand can create "Shapekeys" from mesh deformations caused by "Deformation Bones" but it needs a separate mesh.
In other words: „Shapekey“ creations using just one single mesh are only possible in „Edit Mode“ and are therefore excluding deformations by „Deformation Bones“ done exclusively in „Pose Mode“.
Some "Modifiers" offer the possibility to apply or (only in newer Blender versions) save them as "Shapekeys"
1) "Displacement Modifier"
2) "Armature Modifier"
With the mesh deformations by the "Armature Modifier" now "Saved as Shapekey" (that is the "Armature Modifier" is still in place) and everything set so that only the new "Shapekey" causes the deformation:
Blender 2.66.1 only offered the possibility to "Apply as Shapekey" so that the "Armature Modifier" got deleted:
That's why it was necessary in older Blender versions to use as second mesh and "Join as Shapes" for saving mesh deformations caused by bones as "Shapekeys" without removing the "Armature Modifier". On the other hand, you could manually add an "Armature Modifier" again and set to "Vertex Groups" for the mesh binding (default) since these "Vertex Groups" having the same names as their corresponding "Bones" aren't deleted with the application of the "Armature Modifier".