Optimal reaction pathways for the conversion of renewable feedstocks are often examined by reaction network flux analysis. An alternative modelling approach for reaction networks is a Petri net. These explicitly take the reaction sequence into account. In the optimisation of a network, this can allow the implementation of constraints on circular reaction structures, which are common substructures in chemical reaction networks. In this study, we compare the performance of the models in an illustrative minimal working example of a circular reaction substructure. The reaction network flux analysis is shown to be a relaxation of the Petri net formulation. Most notable, this work contributes to well-reasoned model choices for reaction networks.