Optimal dynamic discrimination (ODD) was recently introduced as a technique for maximally drawing out and detecting the differences between similar quantum systems by exploiting their controllable dynamical properties. As a simulation of ODD, optimal fields were found that successfully discriminated among similar species, but the underlying mechanisms of the process remained obscure. Hamiltonian encoding (HE) has been introduced as a technique for identifying the mechanisms of controlled quantum dynamics. The results of a HE based simulation analysis of ODD are presented in this paper. Different types and degrees of constructive and destructive interference are shown to underly the controlled discrimination processes. In general, it is found that successful discrimination relies on more complex interfering pathways for increasingly similar systems or increasing numbers of similar quantum systems.