What about;
- Moving both models to the center of the scene (origin)
- Creating three orthogonal planes that delineate the local coordinate system (or more like the basis) on both models (e.g. xy1, xz1, yz1, xy2, xz2, yz2)… similar to what you did on your screenshot…
- Calculate the angles between corresponding planes using the Python interactor and this example… this should be equivalent to a dot product between vectors, so the angle will not be tied to the overall coordinate system as in “angle planes” module you are using.
The challenge here is making sure those planes are made with the same features/landmarks on the model. My guess is that you already thought of this though.