You should definitely be able to perform the same kind of calculations as in the paper you mention with QuantumATK! But there is no need at all to extract the MTP parameters for that, nor is it particularly useful even if you could, as they are just a huge number of numerical coefficients without physical meaning. By setting up the right training protocol and fitting the MTP, you will obtain a forcefield model that can be directly used to compute the phonon frequencies, eigenmodes etc, and perform MD calculations, all within QuantumATK itself.
