After a whole lot of hair-pulling, I just managed to get shape keys in place on deformed meshes, both by the Shrinkwrap modifier with “Apply As Shape”, and, more deliciously, on meshes I bent with a little Python script, by using “Join As Shapes”.
This thing is sweet. No corrective shape keys, no VSK1 to VSK2, and no Deformed Mesh to VSK, none of that. Just take your object with no shape keys yet, not even basis, duplicate it, change the shape of the dupe with the script, then select both in the order that the original shape is the active shape, hit the Shape Keys disclosure arrow and go down on Join As Shapes! It automatically generates both the basis key with the basis shape and a key with the duplicate object’s name with its shape. And you’re good to go!
Join As Shapes. It just rocks. Ladies and Gentlemen, that is all. 