Gizmo manager is not resetting internal transform state when you use bakeCurrentTransformIntoVertices. Seems one needs to detach and reattach the gizmo which is unfortunate complexity… is this a bug?
Adding @Cedric but I think it’s expected, when you bake the transform into the vertices, the original matrix is reset to the identity without the gizmo being aware of it.
As said @Evgeni_Popov , the transform is baked into the vertices and the original matrix of the mesh is reset to identity. That’s what is happening if you check the values with the inspector.
But, your mesh is parented to a pivot and baking the vertices doesn’t change at all the pivot transform.
So, when baking, the pivot transform is baked and the pivot transform is then used for rendering.
You have to reset the pivot transform (or any other parent transform) to remove that second transform.