I have enabled deformable model registration as fourth level of registration (scaling, rigid, affine) in FastModelAlign module of SlicerMorph extension. Like ALPACA, it uses the point cloud based registration via Coherent Point Drift (CPD) algorithm. Then pointwise deformations are interpolated for every vertex. In its default mode it works quite fast.
You can also output an interpolated grid transform (up to 256x256x256 grid size, default is 128^3) so that you can apply the resultant transform to an object other the model.
It is new and not tested a lot, but if you want to give it a try it is available starting todays preview builds.
