Since I am looking at the glycosylation process within the Golgi, I need to be able to vary my enzyme concentrations depending on how far I move along the Golgi, i.e. certain enzymes are in higher concentrations at the entry whereas others are in higher concentrations closer to the exit. I do realize that one workaround would be to separate these heterogeneous zones into compartments. However, this adds multiple unknown parameters that contribute to a ballooning parameter estimation problem. Further, recent literature suggests that the Golgi itself matures and the enzymes undergo retrograde transport which cannot be accurately modeled using several compartments.
I have a functional model built in MATLAB, but I greatly favor the mobility that SBML provides.