Thank you for the report! We have a couple of findings:
Issue 1: The problem is that Sprite Skin does not immediately reflect changes in the "GPU Skinning" option in Player settings. Reloading the scene in the editor will reflect the deformation.
Issue 2: The problem is that applying MPB disables the SRP Batcher in the renderer. GPU deformations are only possible with the SRP Batcher enabled.
Issue 3: When using Shader Graph, the Sprite Skinning Node must be set.
To communicate this to the users, we are updating our documentation to reflect this