Here, we take stock of the lessons learned in Ref. to critically compare two different methods of representing the configurations of flexible molecules in a crystal for training invertible flow-based probabilistic generative models (PGMs) that can effectively map between two metastable water ice crystal structures (Ice XI and Ic), modeled with an empirical classical force field. In particular, we assess the efficiency and accuracy of the lattice-free energy estimates obtained by MLenabled targeted free energy estimation against ground truth estimates obtained with an Einstein Crystal method. We examine the effect of different temperatures and system sizes on the convergence of free energy estimates and the quality of extrapolating these results to the thermodynamic limit.