In recent years, significant advancements in computational methods have dramatically enhanced the precision in determining the energetic ranking of different phases of molecular crystals. The developments mainly focused on providing accurate dispersion corrected exchange correlation functionals and methods for describing the vibrational entropy contributions to the free energy at finite temperatures. Several molecular crystals phases were recently found to have of multi-minima character. For our investigations we highlight the multi-minima character in the example of the molecular crystal consisting of N-(4-Methylbenzylidene)-4-methylalanine. We explore its potential energy landscape on the full DFT level or with a machine learned potential that was fitted to DFT data. We calculate not only many local minima but also exact barriers along transformation pathways to demonstrate the multi-minima character of our system. Furthermore, we present a framework, based on the quantum superposition method, that includes both configurational and vibrational entropy. As an example, we show for our system that the transition temperature between two of its phases is afflicted by an error of about 200 K if the multi-minima character is not taken into account. This indicates that it is absolutely essential to consider configurational entropy to obtain reliable finite temperature free energy rankings for complex molecular crystals.